ICGRC Omics API Demo (cannabinoid genes SNP clusters and Hemp/Drug label matching, live query all SNPs)¶

About this notebook Cannabinoid genes SNPs are clustered and compared with legacy hemp/drug samples information

In [1]:
%matplotlib inline
%load_ext autoreload
   
import os
import requests
from IPython.display import display, Image, FileLink
#from jupyter_datatables import init_datatables_mode
#from ipydatagrid import DataGrid
from itables import init_notebook_mode
init_notebook_mode(all_interactive=True)
#init_notebook_mode(connected=True)
import itables.options as itablesopt
# display table options
#itablesopt.lengthMenu = [2, 5, 10, 20, 50, 100, 200, 500]
#itablesopt.maxBytes = 10000 , 0 to disable
#itablesopt.maxRows
#itablesopt.maxColumns

#%load_ext jupyter_require
#%requirejs d3 https://d3js.org/d3.v5.min
#init_datatables_mode()
In [2]:
%autoreload 2
import omics_api
from omics_api import *
In [3]:
REQUERY_URL=False
DEBUGGNG=False
myunit='percent_of_dw'

if DEBUGGNG:
    setVariables(loglevel=getSetting('SHOW_DEBUG'),keep_unit=myunit)
else:
    setVariables(loglevel=getSetting('SHOW_ERRORONLY'),keep_unit=myunit)
#setVariables(loglevel=getSetting('SHOW_ERRORONLY'))

"set variables: \nkeep_unit=percent_of_dw\nr_path=Rscript\nplink_path=plink\nLOG_LEVEL=1\nunit_converter={('percent_of_dw', 'ug_per_gdw'): 10000.0, ('ug_per_gdw', 'percent_of_dw'): 0.0001}"

Gene genes with cannabinoid annotations

In [6]:
urlgenes='https://icgrc.info/api/user/gene/cannabid,cannabic,cannabiv,cannabin?annot=cs10&accession=all' 
labelgenes='cannab_live'
df_raw= read_url(urlgenes, labelgenes,requery=REQUERY_URL)

display(df_raw)
name contig fmin fmax strand gb_keyword go_term interpro_value
Loading... (need help?)

Query each gene region, compare clustering based on SNPs and based on Hemp/Drug sample information. The steps are:

  • Convert SNPs to plink and use plink --cluster ibs, with K=2
  • Collect the samples for each cluster from SNPs
  • Collect the samples for each hemp/drug from the cultivar_group property in sample

For each gene

  • Calculate Variation of Information on the cluster and group partitions generated doi:10.1007/978-3-540-45167-9_14
  • Calculate Jaccard index all cluster-pairs pairs
In [8]:
#setVariables(loglevel=getSetting('SHOW_DEBUG'))
DATADIR='data'
PLINKFILE=DATADIR + '/cs10-merge-wgs7ds-21trich-plink'
PLINKFILE=DATADIR + '/cs10-wgs7ds-genomicsdb-allsnps.isec_cds.snpeff.plink'
PLINKFILE=DATADIR + '/cs10-wgs7ds-genomicsdb-gatk4170.allsnpsonly-bcftools.filltags.fmis7maf05exchet9hwe9.plink'
#draw_heatmap=['LOC115696986', 'LOC115697762']  
vi_jaccard_scores=dict()
gene2range=dict()
for idx,row in df_raw.iterrows():
    reg=row['contig'] + '_' + str(row['fmin']) + '_' + str(row['fmax'])  
    gene2range[row['name']]=(row['contig'],str(row['fmin']),str(row['fmax']),row['name'])
    print(reg + ' ' + row['name'] + ' ' + row['gb_keyword'])
    urlloc='https://icgrc.info/api/user/variant/' + row['contig'] + ':' + str(row['fmin']) + '-' + str(row['fmax']) + '?snpds=7ds&ref=cs10' 
    df_snp= read_url(urlloc,reg,requery=REQUERY_URL)
    #display(df_snp)
    df_hasgroup=df_snp.set_index('property',drop=False)
    df_hasgroup=df_hasgroup.loc[:, df_hasgroup.loc['cultivar_group'].isin([TYPE_PROP,'cultivar_group','Hemp','Drug','BLDT','NLDT','Hemp-type','Drug-type','Drug type feral','Type I','Type III'])]
    df_hasgroup=df_hasgroup.reset_index(drop=True)
    #display(df_hasgroup)
    convert_group={'BLDT':'Drug','NLDT':'Drug','Hemp-type':'Hemp','Drug-type':'Drug','Drug type feral':'Drug','Type I':'Drug','Type III':'Hemp'}
    heatmap=False #row['name'] in draw_heatmap
    #if heatmap:
    #vi_jaccard_scores[row['name'] + ' ' + reg + ' ' + row['gb_keyword']]=do_phylo(df_hasgroup, 'cluster_' + reg,K=2,convert_group=convert_group,plink_file=PLINKFILE,plink_extract=[gene2range[row['name']]],heatmap=heatmap)
    vi_jaccard_scores[row['name'] + ' ' + reg + ' ' + row['gb_keyword']]=do_phylo(df_hasgroup, 'cluster_' + reg,K=2,convert_group=convert_group,heatmap=heatmap)
    #break 
    
listreg=[]
for reg in vi_jaccard_scores.keys():
    print("\n" + reg)
    j=vi_jaccard_scores[reg]
    vi=None
    nvi=None
    J=None
    if not j is None: 
        if j[0]:
            #print("\nvi=" + str(j[0]))
            #print("\njaccard=" + str(j[1]))
            vi=j[0]
            nvi=j[1]
            J=str(j[2])
            #j=(vi, mapGroupClust2Jaccard, mapGroup2Sample,  mapCluster2Sample)
    listreg.append([reg,vi,nvi,J])

import pandas as pd
pdvi1=pd.DataFrame(listreg,columns=['region','VI','Normalized VI','Jaccard'])
display(pdvi1)
pdvi1.to_csv(labelgenes + '_clusters_vi_' + str(1) +'.tsv',sep="\t")

NC_044374.1_52617968_52619389 LOC115717841 cannabidiolic acid synthase-like

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.460890142730908  Normalized VI=0.8648184479451108'
NC_044375.1_15287394_15289081 LOC115718836 tetrahydrocannabinolic acid synthase-like

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.6005237567859867  Normalized VI=0.9728160551987345'
NC_044375.1_15324213_15325849 LOC115720716 tetrahydrocannabinolic acid synthase-like

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.5052184258579917  Normalized VI=0.9347560217007158'
NC_044378.1_25821934_25823723 LOC115697880 inactive tetrahydrocannabinolic acid synthase

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8272324366799668  Normalized VI=0.9792775333023592'
NC_044378.1_25916956_25917584 LOC115696909 inactive tetrahydrocannabinolic acid synthase-like

'common samples  225'
3
'No SNP entry'
NC_044378.1_29635083_29636878 LOC115696884 cannabidiolic acid synthase-like 1

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.845874742069573  Normalized VI=0.9717466231446655'
NC_044378.1_30980884_30982768 LOC115697762 cannabidiolic acid synthase

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.9640497745342672  Normalized VI=0.660402190800954'
NC_044378.1_34047624_34048440 LOC115696987 cannabidiolic acid synthase-like

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.69485651713612  Normalized VI=0.9478771361234601'
NC_044378.1_34056091_34061726 LOC115696986 tetrahydrocannabinolic acid synthase-like

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.9309195491848907  Normalized VI=0.9952737725415531'
NC_044378.1_34132843_34134661 LOC115697126 cannabidiolic acid synthase-like 1

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.5948639808694591  Normalized VI=0.9545312378508469'
NC_044378.1_61398236_61400085 LOC115697019 cannabidiolic acid synthase-like 1

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.6110637734344542  Normalized VI=0.9314586303040842'
LOC115717841 NC_044374.1_52617968_52619389 cannabidiolic acid synthase-like

LOC115718836 NC_044375.1_15287394_15289081 tetrahydrocannabinolic acid synthase-like

LOC115720716 NC_044375.1_15324213_15325849 tetrahydrocannabinolic acid synthase-like

LOC115697880 NC_044378.1_25821934_25823723 inactive tetrahydrocannabinolic acid synthase

LOC115696909 NC_044378.1_25916956_25917584 inactive tetrahydrocannabinolic acid synthase-like

LOC115696884 NC_044378.1_29635083_29636878 cannabidiolic acid synthase-like 1

LOC115697762 NC_044378.1_30980884_30982768 cannabidiolic acid synthase

LOC115696987 NC_044378.1_34047624_34048440 cannabidiolic acid synthase-like

LOC115696986 NC_044378.1_34056091_34061726 tetrahydrocannabinolic acid synthase-like

LOC115697126 NC_044378.1_34132843_34134661 cannabidiolic acid synthase-like 1

LOC115697019 NC_044378.1_61398236_61400085 cannabidiolic acid synthase-like 1
region VI Normalized VI Jaccard
Loading... (need help?)

Repeat for the best (lowest VI) and worst (largest VI)) cluster match, showing heatmap and clusters, and using the API module do_clustering

In [12]:
show_clusters=['LOC115697762','LOC115696986']
convert_group={'BLDT':'Drug','NLDT':'Drug','Hemp-type':'Hemp','Drug-type':'Drug','Drug type feral':'Drug','Type I':'Drug','Type III':'Hemp'}
gene2range=dict()
for idx,row in df_raw.iterrows():
    gene2range[row['name']]=(row['contig'],str(row['fmin']),str(row['fmax']),row['name'])
    if row['name'] in show_clusters:
        reg=row['contig'] + '_' + str(row['fmin']) + '_' + str(row['fmax'])  
        gene2rangei=[(row['contig'],str(row['fmin']),str(row['fmax']),row['name'])]
        print(reg + ' ' + row['name'] + ' ' + row['gb_keyword'])
        urlloc='https://icgrc.info/api/user/variant/' + row['contig'] + ':' + str(row['fmin']) + '-' + str(row['fmax']) + '?snpds=7ds&ref=cs10' 
        df_snp= read_url(urlloc,reg,requery=REQUERY_URL)
        #do_clustering(df_snp,row['name'],'cultivar_group',convert_group=convert_group,K=2,heatmap=True,plink_file=PLINKFILE,plink_extract=gene2rangei)
        do_clustering(df_snp,row['name'],'cultivar_group',convert_group=convert_group,K=2,heatmap=True)

NC_044378.1_30980884_30982768 LOC115697762 cannabidiolic acid synthase

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697762.hmp snp_cluster_LOC115697762.map > snp_cluster_LOC115697762.ped'
Warning: Variant 17 triallelic; setting rarest alleles missing.
Warning: Variant 46 triallelic; setting rarest alleles missing.
Warning: Variant 61 triallelic; setting rarest alleles missing.
Warning: Variant 70 triallelic; setting rarest alleles missing.
Warning: Variant 80 triallelic; setting rarest alleles missing.
Warning: Variant 162 triallelic; setting rarest alleles missing.
Warning: Variant 185 triallelic; setting rarest alleles missing.
Warning: Variant 249 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'bedtools getfasta -fi /home/lmansu10/data/reference/cs10refseq.fna -bed cluster_LOC115697762.btbed > cluster_LOC115697762.bed.ref'
plink --bfile cluster_LOC115697762 --recode tab --out cluster_LOC115697762_ped --allow-extra-chr

'cluster_LOC115697762_ped.ped.tsv  generated'
python draw_tree_matrix.py cluster_LOC115697762_ped.ped.tsv cluster_LOC115697762.newick
Click here to download: type_snpseektree_cluster_LOC115697762.newick.rename.nwk.rr.png
No description has been provided for this image 
'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
NC_044378.1_34056091_34061726 LOC115696986 tetrahydrocannabinolic acid synthase-like

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696986.hmp snp_cluster_LOC115696986.map > snp_cluster_LOC115696986.ped'
Warning: Variant 49 triallelic; setting rarest alleles missing.
Warning: Variant 118 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'bedtools getfasta -fi /home/lmansu10/data/reference/cs10refseq.fna -bed cluster_LOC115696986.btbed > cluster_LOC115696986.bed.ref'
plink --bfile cluster_LOC115696986 --recode tab --out cluster_LOC115696986_ped --allow-extra-chr

'cluster_LOC115696986_ped.ped.tsv  generated'
python draw_tree_matrix.py cluster_LOC115696986_ped.ped.tsv cluster_LOC115696986.newick
Click here to download: type_snpseektree_cluster_LOC115696986.newick.rename.nwk.rr.png
No description has been provided for this image 
'Variation of Information=1.876809108851948  Normalized VI=0.9999890667707702'

Extend by using mutiple G genes combinations

In [15]:
import itertools

G=3
genecombination=list(itertools.combinations(df_raw['name'].tolist(),G))
display(genecombination)

[('LOC115717841', 'LOC115718836', 'LOC115720716'),
 ('LOC115717841', 'LOC115718836', 'LOC115697880'),
 ('LOC115717841', 'LOC115718836', 'LOC115696909'),
 ('LOC115717841', 'LOC115718836', 'LOC115696884'),
 ('LOC115717841', 'LOC115718836', 'LOC115697762'),
 ('LOC115717841', 'LOC115718836', 'LOC115696987'),
 ('LOC115717841', 'LOC115718836', 'LOC115696986'),
 ('LOC115717841', 'LOC115718836', 'LOC115697126'),
 ('LOC115717841', 'LOC115718836', 'LOC115697019'),
 ('LOC115717841', 'LOC115720716', 'LOC115697880'),
 ('LOC115717841', 'LOC115720716', 'LOC115696909'),
 ('LOC115717841', 'LOC115720716', 'LOC115696884'),
 ('LOC115717841', 'LOC115720716', 'LOC115697762'),
 ('LOC115717841', 'LOC115720716', 'LOC115696987'),
 ('LOC115717841', 'LOC115720716', 'LOC115696986'),
 ('LOC115717841', 'LOC115720716', 'LOC115697126'),
 ('LOC115717841', 'LOC115720716', 'LOC115697019'),
 ('LOC115717841', 'LOC115697880', 'LOC115696909'),
 ('LOC115717841', 'LOC115697880', 'LOC115696884'),
 ('LOC115717841', 'LOC115697880', 'LOC115697762'),
 ('LOC115717841', 'LOC115697880', 'LOC115696987'),
 ('LOC115717841', 'LOC115697880', 'LOC115696986'),
 ('LOC115717841', 'LOC115697880', 'LOC115697126'),
 ('LOC115717841', 'LOC115697880', 'LOC115697019'),
 ('LOC115717841', 'LOC115696909', 'LOC115696884'),
 ('LOC115717841', 'LOC115696909', 'LOC115697762'),
 ('LOC115717841', 'LOC115696909', 'LOC115696987'),
 ('LOC115717841', 'LOC115696909', 'LOC115696986'),
 ('LOC115717841', 'LOC115696909', 'LOC115697126'),
 ('LOC115717841', 'LOC115696909', 'LOC115697019'),
 ('LOC115717841', 'LOC115696884', 'LOC115697762'),
 ('LOC115717841', 'LOC115696884', 'LOC115696987'),
 ('LOC115717841', 'LOC115696884', 'LOC115696986'),
 ('LOC115717841', 'LOC115696884', 'LOC115697126'),
 ('LOC115717841', 'LOC115696884', 'LOC115697019'),
 ('LOC115717841', 'LOC115697762', 'LOC115696987'),
 ('LOC115717841', 'LOC115697762', 'LOC115696986'),
 ('LOC115717841', 'LOC115697762', 'LOC115697126'),
 ('LOC115717841', 'LOC115697762', 'LOC115697019'),
 ('LOC115717841', 'LOC115696987', 'LOC115696986'),
 ('LOC115717841', 'LOC115696987', 'LOC115697126'),
 ('LOC115717841', 'LOC115696987', 'LOC115697019'),
 ('LOC115717841', 'LOC115696986', 'LOC115697126'),
 ('LOC115717841', 'LOC115696986', 'LOC115697019'),
 ('LOC115717841', 'LOC115697126', 'LOC115697019'),
 ('LOC115718836', 'LOC115720716', 'LOC115697880'),
 ('LOC115718836', 'LOC115720716', 'LOC115696909'),
 ('LOC115718836', 'LOC115720716', 'LOC115696884'),
 ('LOC115718836', 'LOC115720716', 'LOC115697762'),
 ('LOC115718836', 'LOC115720716', 'LOC115696987'),
 ('LOC115718836', 'LOC115720716', 'LOC115696986'),
 ('LOC115718836', 'LOC115720716', 'LOC115697126'),
 ('LOC115718836', 'LOC115720716', 'LOC115697019'),
 ('LOC115718836', 'LOC115697880', 'LOC115696909'),
 ('LOC115718836', 'LOC115697880', 'LOC115696884'),
 ('LOC115718836', 'LOC115697880', 'LOC115697762'),
 ('LOC115718836', 'LOC115697880', 'LOC115696987'),
 ('LOC115718836', 'LOC115697880', 'LOC115696986'),
 ('LOC115718836', 'LOC115697880', 'LOC115697126'),
 ('LOC115718836', 'LOC115697880', 'LOC115697019'),
 ('LOC115718836', 'LOC115696909', 'LOC115696884'),
 ('LOC115718836', 'LOC115696909', 'LOC115697762'),
 ('LOC115718836', 'LOC115696909', 'LOC115696987'),
 ('LOC115718836', 'LOC115696909', 'LOC115696986'),
 ('LOC115718836', 'LOC115696909', 'LOC115697126'),
 ('LOC115718836', 'LOC115696909', 'LOC115697019'),
 ('LOC115718836', 'LOC115696884', 'LOC115697762'),
 ('LOC115718836', 'LOC115696884', 'LOC115696987'),
 ('LOC115718836', 'LOC115696884', 'LOC115696986'),
 ('LOC115718836', 'LOC115696884', 'LOC115697126'),
 ('LOC115718836', 'LOC115696884', 'LOC115697019'),
 ('LOC115718836', 'LOC115697762', 'LOC115696987'),
 ('LOC115718836', 'LOC115697762', 'LOC115696986'),
 ('LOC115718836', 'LOC115697762', 'LOC115697126'),
 ('LOC115718836', 'LOC115697762', 'LOC115697019'),
 ('LOC115718836', 'LOC115696987', 'LOC115696986'),
 ('LOC115718836', 'LOC115696987', 'LOC115697126'),
 ('LOC115718836', 'LOC115696987', 'LOC115697019'),
 ('LOC115718836', 'LOC115696986', 'LOC115697126'),
 ('LOC115718836', 'LOC115696986', 'LOC115697019'),
 ('LOC115718836', 'LOC115697126', 'LOC115697019'),
 ('LOC115720716', 'LOC115697880', 'LOC115696909'),
 ('LOC115720716', 'LOC115697880', 'LOC115696884'),
 ('LOC115720716', 'LOC115697880', 'LOC115697762'),
 ('LOC115720716', 'LOC115697880', 'LOC115696987'),
 ('LOC115720716', 'LOC115697880', 'LOC115696986'),
 ('LOC115720716', 'LOC115697880', 'LOC115697126'),
 ('LOC115720716', 'LOC115697880', 'LOC115697019'),
 ('LOC115720716', 'LOC115696909', 'LOC115696884'),
 ('LOC115720716', 'LOC115696909', 'LOC115697762'),
 ('LOC115720716', 'LOC115696909', 'LOC115696987'),
 ('LOC115720716', 'LOC115696909', 'LOC115696986'),
 ('LOC115720716', 'LOC115696909', 'LOC115697126'),
 ('LOC115720716', 'LOC115696909', 'LOC115697019'),
 ('LOC115720716', 'LOC115696884', 'LOC115697762'),
 ('LOC115720716', 'LOC115696884', 'LOC115696987'),
 ('LOC115720716', 'LOC115696884', 'LOC115696986'),
 ('LOC115720716', 'LOC115696884', 'LOC115697126'),
 ('LOC115720716', 'LOC115696884', 'LOC115697019'),
 ('LOC115720716', 'LOC115697762', 'LOC115696987'),
 ('LOC115720716', 'LOC115697762', 'LOC115696986'),
 ('LOC115720716', 'LOC115697762', 'LOC115697126'),
 ('LOC115720716', 'LOC115697762', 'LOC115697019'),
 ('LOC115720716', 'LOC115696987', 'LOC115696986'),
 ('LOC115720716', 'LOC115696987', 'LOC115697126'),
 ('LOC115720716', 'LOC115696987', 'LOC115697019'),
 ('LOC115720716', 'LOC115696986', 'LOC115697126'),
 ('LOC115720716', 'LOC115696986', 'LOC115697019'),
 ('LOC115720716', 'LOC115697126', 'LOC115697019'),
 ('LOC115697880', 'LOC115696909', 'LOC115696884'),
 ('LOC115697880', 'LOC115696909', 'LOC115697762'),
 ('LOC115697880', 'LOC115696909', 'LOC115696987'),
 ('LOC115697880', 'LOC115696909', 'LOC115696986'),
 ('LOC115697880', 'LOC115696909', 'LOC115697126'),
 ('LOC115697880', 'LOC115696909', 'LOC115697019'),
 ('LOC115697880', 'LOC115696884', 'LOC115697762'),
 ('LOC115697880', 'LOC115696884', 'LOC115696987'),
 ('LOC115697880', 'LOC115696884', 'LOC115696986'),
 ('LOC115697880', 'LOC115696884', 'LOC115697126'),
 ('LOC115697880', 'LOC115696884', 'LOC115697019'),
 ('LOC115697880', 'LOC115697762', 'LOC115696987'),
 ('LOC115697880', 'LOC115697762', 'LOC115696986'),
 ('LOC115697880', 'LOC115697762', 'LOC115697126'),
 ('LOC115697880', 'LOC115697762', 'LOC115697019'),
 ('LOC115697880', 'LOC115696987', 'LOC115696986'),
 ('LOC115697880', 'LOC115696987', 'LOC115697126'),
 ('LOC115697880', 'LOC115696987', 'LOC115697019'),
 ('LOC115697880', 'LOC115696986', 'LOC115697126'),
 ('LOC115697880', 'LOC115696986', 'LOC115697019'),
 ('LOC115697880', 'LOC115697126', 'LOC115697019'),
 ('LOC115696909', 'LOC115696884', 'LOC115697762'),
 ('LOC115696909', 'LOC115696884', 'LOC115696987'),
 ('LOC115696909', 'LOC115696884', 'LOC115696986'),
 ('LOC115696909', 'LOC115696884', 'LOC115697126'),
 ('LOC115696909', 'LOC115696884', 'LOC115697019'),
 ('LOC115696909', 'LOC115697762', 'LOC115696987'),
 ('LOC115696909', 'LOC115697762', 'LOC115696986'),
 ('LOC115696909', 'LOC115697762', 'LOC115697126'),
 ('LOC115696909', 'LOC115697762', 'LOC115697019'),
 ('LOC115696909', 'LOC115696987', 'LOC115696986'),
 ('LOC115696909', 'LOC115696987', 'LOC115697126'),
 ('LOC115696909', 'LOC115696987', 'LOC115697019'),
 ('LOC115696909', 'LOC115696986', 'LOC115697126'),
 ('LOC115696909', 'LOC115696986', 'LOC115697019'),
 ('LOC115696909', 'LOC115697126', 'LOC115697019'),
 ('LOC115696884', 'LOC115697762', 'LOC115696987'),
 ('LOC115696884', 'LOC115697762', 'LOC115696986'),
 ('LOC115696884', 'LOC115697762', 'LOC115697126'),
 ('LOC115696884', 'LOC115697762', 'LOC115697019'),
 ('LOC115696884', 'LOC115696987', 'LOC115696986'),
 ('LOC115696884', 'LOC115696987', 'LOC115697126'),
 ('LOC115696884', 'LOC115696987', 'LOC115697019'),
 ('LOC115696884', 'LOC115696986', 'LOC115697126'),
 ('LOC115696884', 'LOC115696986', 'LOC115697019'),
 ('LOC115696884', 'LOC115697126', 'LOC115697019'),
 ('LOC115697762', 'LOC115696987', 'LOC115696986'),
 ('LOC115697762', 'LOC115696987', 'LOC115697126'),
 ('LOC115697762', 'LOC115696987', 'LOC115697019'),
 ('LOC115697762', 'LOC115696986', 'LOC115697126'),
 ('LOC115697762', 'LOC115696986', 'LOC115697019'),
 ('LOC115697762', 'LOC115697126', 'LOC115697019'),
 ('LOC115696987', 'LOC115696986', 'LOC115697126'),
 ('LOC115696987', 'LOC115696986', 'LOC115697019'),
 ('LOC115696987', 'LOC115697126', 'LOC115697019'),
 ('LOC115696986', 'LOC115697126', 'LOC115697019')]
In [18]:
vi_jaccard_scores=dict()
#draw_heatmap=['LOC115720716_LOC115696884_LOC115697126','LOC115696884_LOC115697126_LOC115697019','LOC115718836_LOC115697762_LOC115696987']
#draw_heatmap=['LOC115696909_LOC115696987_LOC115696986','LOC115718836_LOC115696987_LOC115696986']
gcount=1
for row in genecombination:

    # query for properties, use one gene
    #gene1=row[0]
    #gene1range=gene2range[gene1]
    regions=[]
    for g in row:
        gene1range=gene2range[g]
        regions.append(gene1range[0] + ':' + gene1range[1] + '-' + gene1range[2])
    regions=",".join(regions)
    
    urlloc='https://icgrc.info/api/user/variant/' + regions + '?snpds=7ds&ref=cs10' 
    #reg=gene1range[0] + '_' + gene1range[1] + '_' + gene1range[2]  
    reg="_".join(row) 
    df_snp= read_url(urlloc,reg,requery=REQUERY_URL)

    reg="_".join(row) 
    plink_extract=[]
    for combs in list(row):
        plink_extract.append(gene2range[combs])
    print(str(gcount) + '/' + str(len(genecombination)) + '  ' + str(plink_extract))
    #vi_jaccard_scores[reg]=do_clustering(df_snp,reg,'cultivar_group',convert_group=convert_group,K=2,heatmap=False,plink_file=PLINKFILE,plink_extract=plink_extract)
    vi_jaccard_scores[reg]=do_clustering(df_snp,reg,'cultivar_group',convert_group=convert_group,K=2,heatmap=False)
    gcount+=1
listreg=[]
for reg in vi_jaccard_scores.keys():
    print("\n" + reg)
    j=vi_jaccard_scores[reg]
    vi=None
    nvi=None
    J=None
    if not j is None: 
        if j[0]:
            vi=j[0]
            nvi=j[1]
            J=str(j[2])
    listreg.append([reg,vi,nvi,J])

pdvi3=pd.DataFrame(listreg,columns=['region','VI','Normalized VI','Jaccard'])
display(pdvi3)
pdvi3.to_csv(labelgenes + '_clusters_vi_' + str(G) +'.tsv',sep="\t")

1/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716')]

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'Variation of Information=1.3835411004404587  Normalized VI=0.8355405365730318'
2/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880')]

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'Variation of Information=1.046533052046446  Normalized VI=0.7418933729612511'
3/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')]

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'Variation of Information=1.583944169411255  Normalized VI=0.902120633812312'
4/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')]

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'Variation of Information=1.1347929377975114  Normalized VI=0.7494446968196167'
5/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

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'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
6/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

Loading required package: MASS
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'Variation of Information=1.5683910382013673  Normalized VI=0.8971008167437493'
7/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

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'Variation of Information=1.8494338585322114  Normalized VI=0.9910610499945303'
8/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

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'Variation of Information=1.2136390288028638  Normalized VI=0.7811778676456225'
9/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

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'Variation of Information=1.0208950974819067  Normalized VI=0.7113916464320327'
10/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880')]

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'Variation of Information=1.3240241781177795  Normalized VI=0.8243233165534178'
11/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')]

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'Variation of Information=1.4863775559348227  Normalized VI=0.8709700950304679'
12/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')]

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'Variation of Information=1.0107093919541599  Normalized VI=0.6972632014015716'
13/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

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'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
14/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

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'Variation of Information=1.5180612669781606  Normalized VI=0.8820767977820962'
15/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

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'Variation of Information=1.7828183852656854  Normalized VI=0.9817123807175844'
16/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

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'Variation of Information=1.598662532421479  Normalized VI=0.9069296153030878'
17/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

Loading required package: MASS
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'Variation of Information=1.0208950974819067  Normalized VI=0.7113916464320327'
18/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')]

Loading required package: MASS
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'Variation of Information=1.733639768650976  Normalized VI=0.9657181335635682'
19/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')]

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'Variation of Information=1.046533052046446  Normalized VI=0.7418933729612511'
20/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

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'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
21/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

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'Variation of Information=1.7260911763450382  Normalized VI=0.9830791363063056'
22/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

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'Variation of Information=1.6822447527338988  Normalized VI=0.9732506606276959'
23/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

Loading required package: MASS
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'Variation of Information=1.7633883530467962  Normalized VI=0.9742174333535991'
24/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

Loading required package: MASS
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'Variation of Information=1.0427111890830973  Normalized VI=0.7053063875959316'
25/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')]

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'Variation of Information=1.560369036519211  Normalized VI=0.8952430565285601'
26/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

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'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
27/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

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'Variation of Information=1.551302772456142  Normalized VI=0.9084907678998714'
28/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

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'Variation of Information=1.8122270595868657  Normalized VI=0.9859656835491462'
29/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

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'Variation of Information=1.524895320137627  Normalized VI=0.9018728073653208'
30/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

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'Variation of Information=0.9549355802393266  Normalized VI=0.6996757581567354'
31/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

Loading required package: MASS
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'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
32/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

Loading required package: MASS
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'Variation of Information=1.4366207441482992  Normalized VI=0.8787467242363695'
33/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

Loading required package: MASS
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'Variation of Information=1.8122270595868657  Normalized VI=0.9859656835491462'
34/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

Loading required package: MASS
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'Variation of Information=1.2207750158610486  Normalized VI=0.7866905445343316'
35/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

Loading required package: MASS
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'Variation of Information=1.1404818832602632  Normalized VI=0.8069288133279894'
36/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

Loading required package: MASS
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'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
37/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

Loading required package: MASS
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'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
38/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

Loading required package: MASS
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'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
39/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

Loading required package: MASS
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'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
40/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
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'Variation of Information=1.9232070654597229  Normalized VI=0.9988442981563539'
41/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

Loading required package: MASS
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'Variation of Information=1.853234236466866  Normalized VI=0.9971526897453865'
42/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
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'Variation of Information=1.1823627239659706  Normalized VI=0.8059314118880573'
43/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

Loading required package: MASS
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Loading 'meta' package (version 6.5-0).
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'Variation of Information=1.8600961528131663  Normalized VI=0.9924582072316522'
44/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

Loading required package: MASS
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Loading 'meta' package (version 6.5-0).
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'Variation of Information=1.8600961528131663  Normalized VI=0.9924582072316522'
45/165  [('NC_044374.1', '52617968', '52619389', 'LOC115717841'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

Loading required package: MASS
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Loading 'meta' package (version 6.5-0).
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'Variation of Information=1.0002964246989674  Normalized VI=0.7105376939179953'
46/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880')]

Loading required package: MASS
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Loading 'meta' package (version 6.5-0).
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'Variation of Information=1.5655078185278404  Normalized VI=0.9190302124941442'
47/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')]

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
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Loading 'meta' package (version 6.5-0).
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'Variation of Information=1.6132984366511027  Normalized VI=0.9410812327405794'
48/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')]

Loading required package: MASS
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Loading 'meta' package (version 6.5-0).
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'Variation of Information=1.6833018628763285  Normalized VI=0.9425858146339652'
49/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

Loading required package: MASS
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'Variation of Information=0.6078016823831691  Normalized VI=0.5036471776371789'
50/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
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Loading 'meta' package (version 6.5-0).
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'Variation of Information=1.7332731502072407  Normalized VI=0.9676297253016208'
51/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

Loading required package: MASS
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'Variation of Information=1.8379167068944906  Normalized VI=0.9895192772277609'
52/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

Loading required package: MASS
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'Variation of Information=1.620184137877324  Normalized VI=0.9282836018714057'
53/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

Loading required package: MASS
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'Variation of Information=0.9358132071015107  Normalized VI=0.6593333920280526'
54/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')]

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
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Loading 'meta' package (version 6.5-0).
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'Variation of Information=1.7356003612885498  Normalized VI=0.9750562002744755'
55/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')]

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
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Loading 'meta' package (version 6.5-0).
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'Variation of Information=1.7295698248773048  Normalized VI=0.9811940069301944'
56/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
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'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
57/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
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'Variation of Information=1.7295698248773048  Normalized VI=0.9811940069301944'
58/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
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'Variation of Information=1.6599812147689925  Normalized VI=0.9697681996990353'
59/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115697880_LOC115697126.hmp snp_cluster_LOC115718836_LOC115697880_LOC115697126.map > snp_cluster_LOC115718836_LOC115697880_LOC115697126.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 143 triallelic; setting rarest alleles missing.
Warning: Variant 147 triallelic; setting rarest alleles missing.
Warning: Variant 224 triallelic; setting rarest alleles missing.
Warning: Variant 225 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.7154474313196313  Normalized VI=0.9520178171719612'
60/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115697880_LOC115697019.hmp snp_cluster_LOC115718836_LOC115697880_LOC115697019.map > snp_cluster_LOC115718836_LOC115697880_LOC115697019.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 143 triallelic; setting rarest alleles missing.
Warning: Variant 147 triallelic; setting rarest alleles missing.
Warning: Variant 260 quadallelic; setting rarest alleles missing.
Warning: Variant 292 triallelic; setting rarest alleles missing.
Warning: Variant 309 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.2136390288028638  Normalized VI=0.7811778676456225'
61/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696909_LOC115696884.hmp snp_cluster_LOC115718836_LOC115696909_LOC115696884.map > snp_cluster_LOC115718836_LOC115696909_LOC115696884.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.7967350035615612  Normalized VI=0.9692659933402339'
62/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696909_LOC115697762.hmp snp_cluster_LOC115718836_LOC115696909_LOC115697762.map > snp_cluster_LOC115718836_LOC115696909_LOC115697762.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 131 triallelic; setting rarest alleles missing.
Warning: Variant 160 triallelic; setting rarest alleles missing.
Warning: Variant 175 triallelic; setting rarest alleles missing.
Warning: Variant 184 triallelic; setting rarest alleles missing.
Warning: Variant 194 triallelic; setting rarest alleles missing.
Warning: Variant 276 triallelic; setting rarest alleles missing.
Warning: Variant 299 triallelic; setting rarest alleles missing.
Warning: Variant 363 triallelic; setting rarest alleles missing.
Warning: Variant 383 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
63/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696909_LOC115696987.hmp snp_cluster_LOC115718836_LOC115696909_LOC115696987.map > snp_cluster_LOC115718836_LOC115696909_LOC115696987.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 115 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8634883758778213  Normalized VI=0.9933691717603476'
64/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696909_LOC115696986.hmp snp_cluster_LOC115718836_LOC115696909_LOC115696986.map > snp_cluster_LOC115718836_LOC115696909_LOC115696986.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 163 triallelic; setting rarest alleles missing.
Warning: Variant 232 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.860096152813166  Normalized VI=0.9924582072316522'
65/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696909_LOC115697126.hmp snp_cluster_LOC115718836_LOC115696909_LOC115697126.map > snp_cluster_LOC115718836_LOC115696909_LOC115697126.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 141 triallelic; setting rarest alleles missing.
Warning: Variant 142 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.5686017132925834  Normalized VI=0.9016816903456666'
66/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696909_LOC115697019.hmp snp_cluster_LOC115718836_LOC115696909_LOC115697019.map > snp_cluster_LOC115718836_LOC115696909_LOC115697019.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 177 quadallelic; setting rarest alleles missing.
Warning: Variant 209 triallelic; setting rarest alleles missing.
Warning: Variant 226 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.3690104767859959  Normalized VI=0.8598452844566867'
67/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696884_LOC115697762.hmp snp_cluster_LOC115718836_LOC115696884_LOC115697762.map > snp_cluster_LOC115718836_LOC115696884_LOC115697762.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 337 triallelic; setting rarest alleles missing.
Warning: Variant 366 triallelic; setting rarest alleles missing.
Warning: Variant 381 triallelic; setting rarest alleles missing.
Warning: Variant 390 triallelic; setting rarest alleles missing.
Warning: Variant 400 triallelic; setting rarest alleles missing.
Warning: Variant 482 triallelic; setting rarest alleles missing.
Warning: Variant 505 triallelic; setting rarest alleles missing.
Warning: Variant 569 triallelic; setting rarest alleles missing.
Warning: Variant 589 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
68/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696884_LOC115696987.hmp snp_cluster_LOC115718836_LOC115696884_LOC115696987.map > snp_cluster_LOC115718836_LOC115696884_LOC115696987.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 321 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.762232934781253  Normalized VI=0.9719846994523406'
69/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696884_LOC115696986.hmp snp_cluster_LOC115718836_LOC115696884_LOC115696986.map > snp_cluster_LOC115718836_LOC115696884_LOC115696986.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 369 triallelic; setting rarest alleles missing.
Warning: Variant 438 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8789331492344872  Normalized VI=0.9948486891367258'
70/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696884_LOC115697126.hmp snp_cluster_LOC115718836_LOC115696884_LOC115697126.map > snp_cluster_LOC115718836_LOC115696884_LOC115697126.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 347 triallelic; setting rarest alleles missing.
Warning: Variant 348 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.6633836166276648  Normalized VI=0.9381270895013021'
71/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696884_LOC115697019.hmp snp_cluster_LOC115718836_LOC115696884_LOC115697019.map > snp_cluster_LOC115718836_LOC115696884_LOC115697019.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 383 quadallelic; setting rarest alleles missing.
Warning: Variant 415 triallelic; setting rarest alleles missing.
Warning: Variant 432 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.972881712027611  Normalized VI=0.6913985130042706'
72/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115697762_LOC115696987.hmp snp_cluster_LOC115718836_LOC115697762_LOC115696987.map > snp_cluster_LOC115718836_LOC115697762_LOC115696987.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 131 triallelic; setting rarest alleles missing.
Warning: Variant 160 triallelic; setting rarest alleles missing.
Warning: Variant 175 triallelic; setting rarest alleles missing.
Warning: Variant 184 triallelic; setting rarest alleles missing.
Warning: Variant 194 triallelic; setting rarest alleles missing.
Warning: Variant 276 triallelic; setting rarest alleles missing.
Warning: Variant 299 triallelic; setting rarest alleles missing.
Warning: Variant 363 triallelic; setting rarest alleles missing.
Warning: Variant 383 triallelic; setting rarest alleles missing.
Warning: Variant 395 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
73/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115697762_LOC115696986.hmp snp_cluster_LOC115718836_LOC115697762_LOC115696986.map > snp_cluster_LOC115718836_LOC115697762_LOC115696986.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 131 triallelic; setting rarest alleles missing.
Warning: Variant 160 triallelic; setting rarest alleles missing.
Warning: Variant 175 triallelic; setting rarest alleles missing.
Warning: Variant 184 triallelic; setting rarest alleles missing.
Warning: Variant 194 triallelic; setting rarest alleles missing.
Warning: Variant 276 triallelic; setting rarest alleles missing.
Warning: Variant 299 triallelic; setting rarest alleles missing.
Warning: Variant 363 triallelic; setting rarest alleles missing.
Warning: Variant 383 triallelic; setting rarest alleles missing.
Warning: Variant 443 triallelic; setting rarest alleles missing.
Warning: Variant 512 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
74/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115697762_LOC115697126.hmp snp_cluster_LOC115718836_LOC115697762_LOC115697126.map > snp_cluster_LOC115718836_LOC115697762_LOC115697126.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 131 triallelic; setting rarest alleles missing.
Warning: Variant 160 triallelic; setting rarest alleles missing.
Warning: Variant 175 triallelic; setting rarest alleles missing.
Warning: Variant 184 triallelic; setting rarest alleles missing.
Warning: Variant 194 triallelic; setting rarest alleles missing.
Warning: Variant 276 triallelic; setting rarest alleles missing.
Warning: Variant 299 triallelic; setting rarest alleles missing.
Warning: Variant 363 triallelic; setting rarest alleles missing.
Warning: Variant 383 triallelic; setting rarest alleles missing.
Warning: Variant 421 triallelic; setting rarest alleles missing.
Warning: Variant 422 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
75/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115697762_LOC115697019.hmp snp_cluster_LOC115718836_LOC115697762_LOC115697019.map > snp_cluster_LOC115718836_LOC115697762_LOC115697019.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 131 triallelic; setting rarest alleles missing.
Warning: Variant 160 triallelic; setting rarest alleles missing.
Warning: Variant 175 triallelic; setting rarest alleles missing.
Warning: Variant 184 triallelic; setting rarest alleles missing.
Warning: Variant 194 triallelic; setting rarest alleles missing.
Warning: Variant 276 triallelic; setting rarest alleles missing.
Warning: Variant 299 triallelic; setting rarest alleles missing.
Warning: Variant 363 triallelic; setting rarest alleles missing.
Warning: Variant 383 triallelic; setting rarest alleles missing.
Warning: Variant 457 quadallelic; setting rarest alleles missing.
Warning: Variant 489 triallelic; setting rarest alleles missing.
Warning: Variant 506 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6078016823831691  Normalized VI=0.5036471776371789'
76/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696987_LOC115696986.hmp snp_cluster_LOC115718836_LOC115696987_LOC115696986.map > snp_cluster_LOC115718836_LOC115696987_LOC115696986.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 115 triallelic; setting rarest alleles missing.
Warning: Variant 212 triallelic; setting rarest alleles missing.
Warning: Variant 281 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.9153232892487821  Normalized VI=0.9982567346958192'
77/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696987_LOC115697126.hmp snp_cluster_LOC115718836_LOC115696987_LOC115697126.map > snp_cluster_LOC115718836_LOC115696987_LOC115697126.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 115 triallelic; setting rarest alleles missing.
Warning: Variant 190 triallelic; setting rarest alleles missing.
Warning: Variant 191 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8634883758778213  Normalized VI=0.9933691717603476'
78/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696987_LOC115697019.hmp snp_cluster_LOC115718836_LOC115696987_LOC115697019.map > snp_cluster_LOC115718836_LOC115696987_LOC115697019.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 115 triallelic; setting rarest alleles missing.
Warning: Variant 226 quadallelic; setting rarest alleles missing.
Warning: Variant 258 triallelic; setting rarest alleles missing.
Warning: Variant 275 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.3557454084706242  Normalized VI=0.860349740649559'
79/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696986_LOC115697126.hmp snp_cluster_LOC115718836_LOC115696986_LOC115697126.map > snp_cluster_LOC115718836_LOC115696986_LOC115697126.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 163 triallelic; setting rarest alleles missing.
Warning: Variant 232 triallelic; setting rarest alleles missing.
Warning: Variant 300 triallelic; setting rarest alleles missing.
Warning: Variant 301 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8600961528131663  Normalized VI=0.9924582072316522'
80/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115696986_LOC115697019.hmp snp_cluster_LOC115718836_LOC115696986_LOC115697019.map > snp_cluster_LOC115718836_LOC115696986_LOC115697019.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 163 triallelic; setting rarest alleles missing.
Warning: Variant 232 triallelic; setting rarest alleles missing.
Warning: Variant 336 quadallelic; setting rarest alleles missing.
Warning: Variant 368 triallelic; setting rarest alleles missing.
Warning: Variant 385 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8699233543203617  Normalized VI=0.9937184807503098'
81/165  [('NC_044375.1', '15287394', '15289081', 'LOC115718836'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115718836_LOC115697126_LOC115697019.hmp snp_cluster_LOC115718836_LOC115697126_LOC115697019.map > snp_cluster_LOC115718836_LOC115697126_LOC115697019.ped'
Warning: Variant 12 triallelic; setting rarest alleles missing.
Warning: Variant 68 triallelic; setting rarest alleles missing.
Warning: Variant 141 triallelic; setting rarest alleles missing.
Warning: Variant 142 triallelic; setting rarest alleles missing.
Warning: Variant 249 quadallelic; setting rarest alleles missing.
Warning: Variant 281 triallelic; setting rarest alleles missing.
Warning: Variant 298 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.0655374806646085  Normalized VI=0.7258274645351408'
82/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115697880_LOC115696909.hmp snp_cluster_LOC115720716_LOC115697880_LOC115696909.map > snp_cluster_LOC115720716_LOC115697880_LOC115696909.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 136 triallelic; setting rarest alleles missing.
Warning: Variant 140 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.7343153747896227  Normalized VI=0.9771828426520263'
83/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115697880_LOC115696884.hmp snp_cluster_LOC115720716_LOC115697880_LOC115696884.map > snp_cluster_LOC115720716_LOC115697880_LOC115696884.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 136 triallelic; setting rarest alleles missing.
Warning: Variant 140 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.702710633294982  Normalized VI=0.9733724603017947'
84/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115697880_LOC115697762.hmp snp_cluster_LOC115720716_LOC115697880_LOC115697762.map > snp_cluster_LOC115720716_LOC115697880_LOC115697762.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 136 triallelic; setting rarest alleles missing.
Warning: Variant 140 triallelic; setting rarest alleles missing.
Warning: Variant 207 triallelic; setting rarest alleles missing.
Warning: Variant 236 triallelic; setting rarest alleles missing.
Warning: Variant 251 triallelic; setting rarest alleles missing.
Warning: Variant 260 triallelic; setting rarest alleles missing.
Warning: Variant 270 triallelic; setting rarest alleles missing.
Warning: Variant 352 triallelic; setting rarest alleles missing.
Warning: Variant 375 triallelic; setting rarest alleles missing.
Warning: Variant 439 triallelic; setting rarest alleles missing.
Warning: Variant 459 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
85/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115697880_LOC115696987.hmp snp_cluster_LOC115720716_LOC115697880_LOC115696987.map > snp_cluster_LOC115720716_LOC115697880_LOC115696987.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 136 triallelic; setting rarest alleles missing.
Warning: Variant 140 triallelic; setting rarest alleles missing.
Warning: Variant 191 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8569044407527913  Normalized VI=0.9963457927078924'
86/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115697880_LOC115696986.hmp snp_cluster_LOC115720716_LOC115697880_LOC115696986.map > snp_cluster_LOC115720716_LOC115697880_LOC115696986.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 136 triallelic; setting rarest alleles missing.
Warning: Variant 140 triallelic; setting rarest alleles missing.
Warning: Variant 239 triallelic; setting rarest alleles missing.
Warning: Variant 308 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.860096152813166  Normalized VI=0.9924582072316522'
87/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115697880_LOC115697126.hmp snp_cluster_LOC115720716_LOC115697880_LOC115697126.map > snp_cluster_LOC115720716_LOC115697880_LOC115697126.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 136 triallelic; setting rarest alleles missing.
Warning: Variant 140 triallelic; setting rarest alleles missing.
Warning: Variant 217 triallelic; setting rarest alleles missing.
Warning: Variant 218 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.7295698248773048  Normalized VI=0.9811940069301944'
88/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115697880_LOC115697019.hmp snp_cluster_LOC115720716_LOC115697880_LOC115697019.map > snp_cluster_LOC115720716_LOC115697880_LOC115697019.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 136 triallelic; setting rarest alleles missing.
Warning: Variant 140 triallelic; setting rarest alleles missing.
Warning: Variant 253 quadallelic; setting rarest alleles missing.
Warning: Variant 285 triallelic; setting rarest alleles missing.
Warning: Variant 302 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.1054986367329496  Normalized VI=0.7482885898111185'
89/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696909_LOC115696884.hmp snp_cluster_LOC115720716_LOC115696909_LOC115696884.map > snp_cluster_LOC115720716_LOC115696909_LOC115696884.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.195157467702955  Normalized VI=0.8428553261946453'
90/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696909_LOC115697762.hmp snp_cluster_LOC115720716_LOC115696909_LOC115697762.map > snp_cluster_LOC115720716_LOC115696909_LOC115697762.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 124 triallelic; setting rarest alleles missing.
Warning: Variant 153 triallelic; setting rarest alleles missing.
Warning: Variant 168 triallelic; setting rarest alleles missing.
Warning: Variant 177 triallelic; setting rarest alleles missing.
Warning: Variant 187 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 292 triallelic; setting rarest alleles missing.
Warning: Variant 356 triallelic; setting rarest alleles missing.
Warning: Variant 376 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
91/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696909_LOC115696987.hmp snp_cluster_LOC115720716_LOC115696909_LOC115696987.map > snp_cluster_LOC115720716_LOC115696909_LOC115696987.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 108 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.7885896276981759  Normalized VI=0.9813090116944699'
92/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696909_LOC115696986.hmp snp_cluster_LOC115720716_LOC115696909_LOC115696986.map > snp_cluster_LOC115720716_LOC115696909_LOC115696986.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 156 triallelic; setting rarest alleles missing.
Warning: Variant 225 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8523005502675205  Normalized VI=0.9934168393329197'
93/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696909_LOC115697126.hmp snp_cluster_LOC115720716_LOC115696909_LOC115697126.map > snp_cluster_LOC115720716_LOC115696909_LOC115697126.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 134 triallelic; setting rarest alleles missing.
Warning: Variant 135 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.0901048337737043  Normalized VI=0.8188866114037845'
94/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696909_LOC115697019.hmp snp_cluster_LOC115720716_LOC115696909_LOC115697019.map > snp_cluster_LOC115720716_LOC115696909_LOC115697019.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 170 quadallelic; setting rarest alleles missing.
Warning: Variant 202 triallelic; setting rarest alleles missing.
Warning: Variant 219 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.06782085453262  Normalized VI=0.7179188867918012'
95/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696884_LOC115697762.hmp snp_cluster_LOC115720716_LOC115696884_LOC115697762.map > snp_cluster_LOC115720716_LOC115696884_LOC115697762.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 330 triallelic; setting rarest alleles missing.
Warning: Variant 359 triallelic; setting rarest alleles missing.
Warning: Variant 374 triallelic; setting rarest alleles missing.
Warning: Variant 383 triallelic; setting rarest alleles missing.
Warning: Variant 393 triallelic; setting rarest alleles missing.
Warning: Variant 475 triallelic; setting rarest alleles missing.
Warning: Variant 498 triallelic; setting rarest alleles missing.
Warning: Variant 562 triallelic; setting rarest alleles missing.
Warning: Variant 582 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
96/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696884_LOC115696987.hmp snp_cluster_LOC115720716_LOC115696884_LOC115696987.map > snp_cluster_LOC115720716_LOC115696884_LOC115696987.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 314 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.7361700071390114  Normalized VI=0.9728478115167104'
97/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696884_LOC115696986.hmp snp_cluster_LOC115720716_LOC115696884_LOC115696986.map > snp_cluster_LOC115720716_LOC115696884_LOC115696986.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 362 triallelic; setting rarest alleles missing.
Warning: Variant 431 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8523005502675205  Normalized VI=0.9934168393329197'
98/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696884_LOC115697126.hmp snp_cluster_LOC115720716_LOC115696884_LOC115697126.map > snp_cluster_LOC115720716_LOC115696884_LOC115697126.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 340 triallelic; setting rarest alleles missing.
Warning: Variant 341 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.9811151472668205  Normalized VI=0.7066047353151121'
99/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696884_LOC115697019.hmp snp_cluster_LOC115720716_LOC115696884_LOC115697019.map > snp_cluster_LOC115720716_LOC115696884_LOC115697019.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 376 quadallelic; setting rarest alleles missing.
Warning: Variant 408 triallelic; setting rarest alleles missing.
Warning: Variant 425 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.1692839541860234  Normalized VI=0.7623257672238246'
100/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115697762_LOC115696987.hmp snp_cluster_LOC115720716_LOC115697762_LOC115696987.map > snp_cluster_LOC115720716_LOC115697762_LOC115696987.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 124 triallelic; setting rarest alleles missing.
Warning: Variant 153 triallelic; setting rarest alleles missing.
Warning: Variant 168 triallelic; setting rarest alleles missing.
Warning: Variant 177 triallelic; setting rarest alleles missing.
Warning: Variant 187 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 292 triallelic; setting rarest alleles missing.
Warning: Variant 356 triallelic; setting rarest alleles missing.
Warning: Variant 376 triallelic; setting rarest alleles missing.
Warning: Variant 388 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
101/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115697762_LOC115696986.hmp snp_cluster_LOC115720716_LOC115697762_LOC115696986.map > snp_cluster_LOC115720716_LOC115697762_LOC115696986.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 124 triallelic; setting rarest alleles missing.
Warning: Variant 153 triallelic; setting rarest alleles missing.
Warning: Variant 168 triallelic; setting rarest alleles missing.
Warning: Variant 177 triallelic; setting rarest alleles missing.
Warning: Variant 187 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 292 triallelic; setting rarest alleles missing.
Warning: Variant 356 triallelic; setting rarest alleles missing.
Warning: Variant 376 triallelic; setting rarest alleles missing.
Warning: Variant 436 triallelic; setting rarest alleles missing.
Warning: Variant 505 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
102/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115697762_LOC115697126.hmp snp_cluster_LOC115720716_LOC115697762_LOC115697126.map > snp_cluster_LOC115720716_LOC115697762_LOC115697126.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 124 triallelic; setting rarest alleles missing.
Warning: Variant 153 triallelic; setting rarest alleles missing.
Warning: Variant 168 triallelic; setting rarest alleles missing.
Warning: Variant 177 triallelic; setting rarest alleles missing.
Warning: Variant 187 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 292 triallelic; setting rarest alleles missing.
Warning: Variant 356 triallelic; setting rarest alleles missing.
Warning: Variant 376 triallelic; setting rarest alleles missing.
Warning: Variant 414 triallelic; setting rarest alleles missing.
Warning: Variant 415 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
103/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115697762_LOC115697019.hmp snp_cluster_LOC115720716_LOC115697762_LOC115697019.map > snp_cluster_LOC115720716_LOC115697762_LOC115697019.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 124 triallelic; setting rarest alleles missing.
Warning: Variant 153 triallelic; setting rarest alleles missing.
Warning: Variant 168 triallelic; setting rarest alleles missing.
Warning: Variant 177 triallelic; setting rarest alleles missing.
Warning: Variant 187 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 292 triallelic; setting rarest alleles missing.
Warning: Variant 356 triallelic; setting rarest alleles missing.
Warning: Variant 376 triallelic; setting rarest alleles missing.
Warning: Variant 450 quadallelic; setting rarest alleles missing.
Warning: Variant 482 triallelic; setting rarest alleles missing.
Warning: Variant 499 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
104/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696987_LOC115696986.hmp snp_cluster_LOC115720716_LOC115696987_LOC115696986.map > snp_cluster_LOC115720716_LOC115696987_LOC115696986.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 108 triallelic; setting rarest alleles missing.
Warning: Variant 205 triallelic; setting rarest alleles missing.
Warning: Variant 274 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8255226409531125  Normalized VI=0.987824129460222'
105/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696987_LOC115697126.hmp snp_cluster_LOC115720716_LOC115696987_LOC115697126.map > snp_cluster_LOC115720716_LOC115696987_LOC115697126.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 108 triallelic; setting rarest alleles missing.
Warning: Variant 183 triallelic; setting rarest alleles missing.
Warning: Variant 184 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8642509055695178  Normalized VI=0.9909264782077022'
106/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696987_LOC115697019.hmp snp_cluster_LOC115720716_LOC115696987_LOC115697019.map > snp_cluster_LOC115720716_LOC115696987_LOC115697019.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 108 triallelic; setting rarest alleles missing.
Warning: Variant 219 quadallelic; setting rarest alleles missing.
Warning: Variant 251 triallelic; setting rarest alleles missing.
Warning: Variant 268 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.0088169209569022  Normalized VI=0.6910898721564807'
107/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696986_LOC115697126.hmp snp_cluster_LOC115720716_LOC115696986_LOC115697126.map > snp_cluster_LOC115720716_LOC115696986_LOC115697126.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 156 triallelic; setting rarest alleles missing.
Warning: Variant 225 triallelic; setting rarest alleles missing.
Warning: Variant 293 triallelic; setting rarest alleles missing.
Warning: Variant 294 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8600961528131663  Normalized VI=0.9924582072316522'
108/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115696986_LOC115697019.hmp snp_cluster_LOC115720716_LOC115696986_LOC115697019.map > snp_cluster_LOC115720716_LOC115696986_LOC115697019.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 156 triallelic; setting rarest alleles missing.
Warning: Variant 225 triallelic; setting rarest alleles missing.
Warning: Variant 329 quadallelic; setting rarest alleles missing.
Warning: Variant 361 triallelic; setting rarest alleles missing.
Warning: Variant 378 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8494338585322114  Normalized VI=0.9910610499945303'
109/165  [('NC_044375.1', '15324213', '15325849', 'LOC115720716'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115720716_LOC115697126_LOC115697019.hmp snp_cluster_LOC115720716_LOC115697126_LOC115697019.map > snp_cluster_LOC115720716_LOC115697126_LOC115697019.ped'
Warning: Variant 63 triallelic; setting rarest alleles missing.
Warning: Variant 134 triallelic; setting rarest alleles missing.
Warning: Variant 135 triallelic; setting rarest alleles missing.
Warning: Variant 242 quadallelic; setting rarest alleles missing.
Warning: Variant 274 triallelic; setting rarest alleles missing.
Warning: Variant 291 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.0427111890830973  Normalized VI=0.7053063875959316'
110/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696909_LOC115696884.hmp snp_cluster_LOC115697880_LOC115696909_LOC115696884.map > snp_cluster_LOC115697880_LOC115696909_LOC115696884.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.697357988469528  Normalized VI=0.9777198925859791'
111/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696909_LOC115697762.hmp snp_cluster_LOC115697880_LOC115696909_LOC115697762.map > snp_cluster_LOC115697880_LOC115696909_LOC115697762.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 100 triallelic; setting rarest alleles missing.
Warning: Variant 129 triallelic; setting rarest alleles missing.
Warning: Variant 144 triallelic; setting rarest alleles missing.
Warning: Variant 153 triallelic; setting rarest alleles missing.
Warning: Variant 163 triallelic; setting rarest alleles missing.
Warning: Variant 245 triallelic; setting rarest alleles missing.
Warning: Variant 268 triallelic; setting rarest alleles missing.
Warning: Variant 332 triallelic; setting rarest alleles missing.
Warning: Variant 352 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
112/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696909_LOC115696987.hmp snp_cluster_LOC115697880_LOC115696909_LOC115696987.map > snp_cluster_LOC115697880_LOC115696909_LOC115696987.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 84 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.859831913264143  Normalized VI=0.9954456293246897'
113/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696909_LOC115696986.hmp snp_cluster_LOC115697880_LOC115696909_LOC115696986.map > snp_cluster_LOC115697880_LOC115696909_LOC115696986.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 132 triallelic; setting rarest alleles missing.
Warning: Variant 201 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.6885807447995387  Normalized VI=0.981627338101568'
114/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696909_LOC115697126.hmp snp_cluster_LOC115697880_LOC115696909_LOC115697126.map > snp_cluster_LOC115697880_LOC115696909_LOC115697126.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 110 triallelic; setting rarest alleles missing.
Warning: Variant 111 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.7295698248773048  Normalized VI=0.9811940069301944'
115/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696909_LOC115697019.hmp snp_cluster_LOC115697880_LOC115696909_LOC115697019.map > snp_cluster_LOC115697880_LOC115696909_LOC115697019.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 146 quadallelic; setting rarest alleles missing.
Warning: Variant 178 triallelic; setting rarest alleles missing.
Warning: Variant 195 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.7154474313196313  Normalized VI=0.9520178171719612'
116/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696884_LOC115697762.hmp snp_cluster_LOC115697880_LOC115696884_LOC115697762.map > snp_cluster_LOC115697880_LOC115696884_LOC115697762.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 306 triallelic; setting rarest alleles missing.
Warning: Variant 335 triallelic; setting rarest alleles missing.
Warning: Variant 350 triallelic; setting rarest alleles missing.
Warning: Variant 359 triallelic; setting rarest alleles missing.
Warning: Variant 369 triallelic; setting rarest alleles missing.
Warning: Variant 451 triallelic; setting rarest alleles missing.
Warning: Variant 474 triallelic; setting rarest alleles missing.
Warning: Variant 538 triallelic; setting rarest alleles missing.
Warning: Variant 558 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.9152610547637542  Normalized VI=0.6529120639677912'
117/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696884_LOC115696987.hmp snp_cluster_LOC115697880_LOC115696884_LOC115696987.map > snp_cluster_LOC115697880_LOC115696884_LOC115696987.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 290 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8620243947966304  Normalized VI=0.9944532239425202'
118/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696884_LOC115696986.hmp snp_cluster_LOC115697880_LOC115696884_LOC115696986.map > snp_cluster_LOC115697880_LOC115696884_LOC115696986.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 338 triallelic; setting rarest alleles missing.
Warning: Variant 407 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.682244752733899  Normalized VI=0.9732506606276959'
119/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696884_LOC115697126.hmp snp_cluster_LOC115697880_LOC115696884_LOC115697126.map > snp_cluster_LOC115697880_LOC115696884_LOC115697126.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 316 triallelic; setting rarest alleles missing.
Warning: Variant 317 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.7505975219858088  Normalized VI=0.9621406627814976'
120/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696884_LOC115697019.hmp snp_cluster_LOC115697880_LOC115696884_LOC115697019.map > snp_cluster_LOC115697880_LOC115696884_LOC115697019.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 352 quadallelic; setting rarest alleles missing.
Warning: Variant 384 triallelic; setting rarest alleles missing.
Warning: Variant 401 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.2545233785618244  Normalized VI=0.798324799772982'
121/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115697762_LOC115696987.hmp snp_cluster_LOC115697880_LOC115697762_LOC115696987.map > snp_cluster_LOC115697880_LOC115697762_LOC115696987.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 100 triallelic; setting rarest alleles missing.
Warning: Variant 129 triallelic; setting rarest alleles missing.
Warning: Variant 144 triallelic; setting rarest alleles missing.
Warning: Variant 153 triallelic; setting rarest alleles missing.
Warning: Variant 163 triallelic; setting rarest alleles missing.
Warning: Variant 245 triallelic; setting rarest alleles missing.
Warning: Variant 268 triallelic; setting rarest alleles missing.
Warning: Variant 332 triallelic; setting rarest alleles missing.
Warning: Variant 352 triallelic; setting rarest alleles missing.
Warning: Variant 364 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
122/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115697762_LOC115696986.hmp snp_cluster_LOC115697880_LOC115697762_LOC115696986.map > snp_cluster_LOC115697880_LOC115697762_LOC115696986.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 100 triallelic; setting rarest alleles missing.
Warning: Variant 129 triallelic; setting rarest alleles missing.
Warning: Variant 144 triallelic; setting rarest alleles missing.
Warning: Variant 153 triallelic; setting rarest alleles missing.
Warning: Variant 163 triallelic; setting rarest alleles missing.
Warning: Variant 245 triallelic; setting rarest alleles missing.
Warning: Variant 268 triallelic; setting rarest alleles missing.
Warning: Variant 332 triallelic; setting rarest alleles missing.
Warning: Variant 352 triallelic; setting rarest alleles missing.
Warning: Variant 412 triallelic; setting rarest alleles missing.
Warning: Variant 481 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
123/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115697762_LOC115697126.hmp snp_cluster_LOC115697880_LOC115697762_LOC115697126.map > snp_cluster_LOC115697880_LOC115697762_LOC115697126.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 100 triallelic; setting rarest alleles missing.
Warning: Variant 129 triallelic; setting rarest alleles missing.
Warning: Variant 144 triallelic; setting rarest alleles missing.
Warning: Variant 153 triallelic; setting rarest alleles missing.
Warning: Variant 163 triallelic; setting rarest alleles missing.
Warning: Variant 245 triallelic; setting rarest alleles missing.
Warning: Variant 268 triallelic; setting rarest alleles missing.
Warning: Variant 332 triallelic; setting rarest alleles missing.
Warning: Variant 352 triallelic; setting rarest alleles missing.
Warning: Variant 390 triallelic; setting rarest alleles missing.
Warning: Variant 391 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
124/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115697762_LOC115697019.hmp snp_cluster_LOC115697880_LOC115697762_LOC115697019.map > snp_cluster_LOC115697880_LOC115697762_LOC115697019.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 100 triallelic; setting rarest alleles missing.
Warning: Variant 129 triallelic; setting rarest alleles missing.
Warning: Variant 144 triallelic; setting rarest alleles missing.
Warning: Variant 153 triallelic; setting rarest alleles missing.
Warning: Variant 163 triallelic; setting rarest alleles missing.
Warning: Variant 245 triallelic; setting rarest alleles missing.
Warning: Variant 268 triallelic; setting rarest alleles missing.
Warning: Variant 332 triallelic; setting rarest alleles missing.
Warning: Variant 352 triallelic; setting rarest alleles missing.
Warning: Variant 426 quadallelic; setting rarest alleles missing.
Warning: Variant 458 triallelic; setting rarest alleles missing.
Warning: Variant 475 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.9152610547637542  Normalized VI=0.6529120639677912'
125/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696987_LOC115696986.hmp snp_cluster_LOC115697880_LOC115696987_LOC115696986.map > snp_cluster_LOC115697880_LOC115696987_LOC115696986.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 84 triallelic; setting rarest alleles missing.
Warning: Variant 181 triallelic; setting rarest alleles missing.
Warning: Variant 250 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.7452182173338375  Normalized VI=0.9885881086871704'
126/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696987_LOC115697126.hmp snp_cluster_LOC115697880_LOC115696987_LOC115697126.map > snp_cluster_LOC115697880_LOC115696987_LOC115697126.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 84 triallelic; setting rarest alleles missing.
Warning: Variant 159 triallelic; setting rarest alleles missing.
Warning: Variant 160 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.859831913264143  Normalized VI=0.9954456293246897'
127/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696987_LOC115697019.hmp snp_cluster_LOC115697880_LOC115696987_LOC115697019.map > snp_cluster_LOC115697880_LOC115696987_LOC115697019.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 84 triallelic; setting rarest alleles missing.
Warning: Variant 195 quadallelic; setting rarest alleles missing.
Warning: Variant 227 triallelic; setting rarest alleles missing.
Warning: Variant 244 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.7776354906115315  Normalized VI=0.9684222314650562'
128/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696986_LOC115697126.hmp snp_cluster_LOC115697880_LOC115696986_LOC115697126.map > snp_cluster_LOC115697880_LOC115696986_LOC115697126.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 132 triallelic; setting rarest alleles missing.
Warning: Variant 201 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 270 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.7718394149517995  Normalized VI=0.9830111120506523'
129/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115696986_LOC115697019.hmp snp_cluster_LOC115697880_LOC115696986_LOC115697019.map > snp_cluster_LOC115697880_LOC115696986_LOC115697019.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 132 triallelic; setting rarest alleles missing.
Warning: Variant 201 triallelic; setting rarest alleles missing.
Warning: Variant 305 quadallelic; setting rarest alleles missing.
Warning: Variant 337 triallelic; setting rarest alleles missing.
Warning: Variant 354 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.6112224700137672  Normalized VI=0.9616762190495045'
130/165  [('NC_044378.1', '25821934', '25823723', 'LOC115697880'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697880_LOC115697126_LOC115697019.hmp snp_cluster_LOC115697880_LOC115697126_LOC115697019.map > snp_cluster_LOC115697880_LOC115697126_LOC115697019.ped'
Warning: Variant 29 triallelic; setting rarest alleles missing.
Warning: Variant 33 triallelic; setting rarest alleles missing.
Warning: Variant 110 triallelic; setting rarest alleles missing.
Warning: Variant 111 triallelic; setting rarest alleles missing.
Warning: Variant 218 quadallelic; setting rarest alleles missing.
Warning: Variant 250 triallelic; setting rarest alleles missing.
Warning: Variant 267 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.246076817595732  Normalized VI=0.7925517208952992'
131/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115696884_LOC115697762.hmp snp_cluster_LOC115696909_LOC115696884_LOC115697762.map > snp_cluster_LOC115696909_LOC115696884_LOC115697762.ped'
Warning: Variant 223 triallelic; setting rarest alleles missing.
Warning: Variant 252 triallelic; setting rarest alleles missing.
Warning: Variant 267 triallelic; setting rarest alleles missing.
Warning: Variant 276 triallelic; setting rarest alleles missing.
Warning: Variant 286 triallelic; setting rarest alleles missing.
Warning: Variant 368 triallelic; setting rarest alleles missing.
Warning: Variant 391 triallelic; setting rarest alleles missing.
Warning: Variant 455 triallelic; setting rarest alleles missing.
Warning: Variant 475 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
132/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115696884_LOC115696987.hmp snp_cluster_LOC115696909_LOC115696884_LOC115696987.map > snp_cluster_LOC115696909_LOC115696884_LOC115696987.ped'
Warning: Variant 207 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8777784073370816  Normalized VI=0.9945413167421732'
133/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115696884_LOC115696986.hmp snp_cluster_LOC115696909_LOC115696884_LOC115696986.map > snp_cluster_LOC115696909_LOC115696884_LOC115696986.ped'
Warning: Variant 255 triallelic; setting rarest alleles missing.
Warning: Variant 324 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8494338585322114  Normalized VI=0.9910610499945303'
134/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115696884_LOC115697126.hmp snp_cluster_LOC115696909_LOC115696884_LOC115697126.map > snp_cluster_LOC115696909_LOC115696884_LOC115697126.ped'
Warning: Variant 233 triallelic; setting rarest alleles missing.
Warning: Variant 234 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.1602357636566856  Normalized VI=0.8194135137242435'
135/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115696884_LOC115697019.hmp snp_cluster_LOC115696909_LOC115696884_LOC115697019.map > snp_cluster_LOC115696909_LOC115696884_LOC115697019.ped'
Warning: Variant 269 quadallelic; setting rarest alleles missing.
Warning: Variant 301 triallelic; setting rarest alleles missing.
Warning: Variant 318 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.0493851723970038  Normalized VI=0.7131521426491578'
136/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115697762_LOC115696987.hmp snp_cluster_LOC115696909_LOC115697762_LOC115696987.map > snp_cluster_LOC115696909_LOC115697762_LOC115696987.ped'
Warning: Variant 17 triallelic; setting rarest alleles missing.
Warning: Variant 46 triallelic; setting rarest alleles missing.
Warning: Variant 61 triallelic; setting rarest alleles missing.
Warning: Variant 70 triallelic; setting rarest alleles missing.
Warning: Variant 80 triallelic; setting rarest alleles missing.
Warning: Variant 162 triallelic; setting rarest alleles missing.
Warning: Variant 185 triallelic; setting rarest alleles missing.
Warning: Variant 249 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 281 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
137/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115697762_LOC115696986.hmp snp_cluster_LOC115696909_LOC115697762_LOC115696986.map > snp_cluster_LOC115696909_LOC115697762_LOC115696986.ped'
Warning: Variant 17 triallelic; setting rarest alleles missing.
Warning: Variant 46 triallelic; setting rarest alleles missing.
Warning: Variant 61 triallelic; setting rarest alleles missing.
Warning: Variant 70 triallelic; setting rarest alleles missing.
Warning: Variant 80 triallelic; setting rarest alleles missing.
Warning: Variant 162 triallelic; setting rarest alleles missing.
Warning: Variant 185 triallelic; setting rarest alleles missing.
Warning: Variant 249 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 329 triallelic; setting rarest alleles missing.
Warning: Variant 398 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
138/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115697762_LOC115697126.hmp snp_cluster_LOC115696909_LOC115697762_LOC115697126.map > snp_cluster_LOC115696909_LOC115697762_LOC115697126.ped'
Warning: Variant 17 triallelic; setting rarest alleles missing.
Warning: Variant 46 triallelic; setting rarest alleles missing.
Warning: Variant 61 triallelic; setting rarest alleles missing.
Warning: Variant 70 triallelic; setting rarest alleles missing.
Warning: Variant 80 triallelic; setting rarest alleles missing.
Warning: Variant 162 triallelic; setting rarest alleles missing.
Warning: Variant 185 triallelic; setting rarest alleles missing.
Warning: Variant 249 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 307 triallelic; setting rarest alleles missing.
Warning: Variant 308 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
139/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115697762_LOC115697019.hmp snp_cluster_LOC115696909_LOC115697762_LOC115697019.map > snp_cluster_LOC115696909_LOC115697762_LOC115697019.ped'
Warning: Variant 17 triallelic; setting rarest alleles missing.
Warning: Variant 46 triallelic; setting rarest alleles missing.
Warning: Variant 61 triallelic; setting rarest alleles missing.
Warning: Variant 70 triallelic; setting rarest alleles missing.
Warning: Variant 80 triallelic; setting rarest alleles missing.
Warning: Variant 162 triallelic; setting rarest alleles missing.
Warning: Variant 185 triallelic; setting rarest alleles missing.
Warning: Variant 249 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 343 quadallelic; setting rarest alleles missing.
Warning: Variant 375 triallelic; setting rarest alleles missing.
Warning: Variant 392 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
140/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115696987_LOC115696986.hmp snp_cluster_LOC115696909_LOC115696987_LOC115696986.map > snp_cluster_LOC115696909_LOC115696987_LOC115696986.ped'
Warning: Variant 1 triallelic; setting rarest alleles missing.
Warning: Variant 98 triallelic; setting rarest alleles missing.
Warning: Variant 167 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8523005502675205  Normalized VI=0.9934168393329197'
141/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115696987_LOC115697126.hmp snp_cluster_LOC115696909_LOC115696987_LOC115697126.map > snp_cluster_LOC115696909_LOC115696987_LOC115697126.ped'
Warning: Variant 1 triallelic; setting rarest alleles missing.
Warning: Variant 76 triallelic; setting rarest alleles missing.
Warning: Variant 77 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8634883758778213  Normalized VI=0.9933691717603476'
142/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115696987_LOC115697019.hmp snp_cluster_LOC115696909_LOC115696987_LOC115697019.map > snp_cluster_LOC115696909_LOC115696987_LOC115697019.ped'
Warning: Variant 1 triallelic; setting rarest alleles missing.
Warning: Variant 112 quadallelic; setting rarest alleles missing.
Warning: Variant 144 triallelic; setting rarest alleles missing.
Warning: Variant 161 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.9732304765975552  Normalized VI=0.6758129552476578'
143/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115696986_LOC115697126.hmp snp_cluster_LOC115696909_LOC115696986_LOC115697126.map > snp_cluster_LOC115696909_LOC115696986_LOC115697126.ped'
Warning: Variant 49 triallelic; setting rarest alleles missing.
Warning: Variant 118 triallelic; setting rarest alleles missing.
Warning: Variant 186 triallelic; setting rarest alleles missing.
Warning: Variant 187 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.887141327621018  Normalized VI=0.995854834300015'
144/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115696986_LOC115697019.hmp snp_cluster_LOC115696909_LOC115696986_LOC115697019.map > snp_cluster_LOC115696909_LOC115696986_LOC115697019.ped'
Warning: Variant 49 triallelic; setting rarest alleles missing.
Warning: Variant 118 triallelic; setting rarest alleles missing.
Warning: Variant 222 quadallelic; setting rarest alleles missing.
Warning: Variant 254 triallelic; setting rarest alleles missing.
Warning: Variant 271 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8699233543203617  Normalized VI=0.9937184807503098'
145/165  [('NC_044378.1', '25916956', '25917584', 'LOC115696909'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696909_LOC115697126_LOC115697019.hmp snp_cluster_LOC115696909_LOC115697126_LOC115697019.map > snp_cluster_LOC115696909_LOC115697126_LOC115697019.ped'
Warning: Variant 27 triallelic; setting rarest alleles missing.
Warning: Variant 28 triallelic; setting rarest alleles missing.
Warning: Variant 135 quadallelic; setting rarest alleles missing.
Warning: Variant 167 triallelic; setting rarest alleles missing.
Warning: Variant 184 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.3699735965415714  Normalized VI=0.8311055170703958'
146/165  [('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696884_LOC115697762_LOC115696987.hmp snp_cluster_LOC115696884_LOC115697762_LOC115696987.map > snp_cluster_LOC115696884_LOC115697762_LOC115696987.ped'
Warning: Variant 223 triallelic; setting rarest alleles missing.
Warning: Variant 252 triallelic; setting rarest alleles missing.
Warning: Variant 267 triallelic; setting rarest alleles missing.
Warning: Variant 276 triallelic; setting rarest alleles missing.
Warning: Variant 286 triallelic; setting rarest alleles missing.
Warning: Variant 368 triallelic; setting rarest alleles missing.
Warning: Variant 391 triallelic; setting rarest alleles missing.
Warning: Variant 455 triallelic; setting rarest alleles missing.
Warning: Variant 475 triallelic; setting rarest alleles missing.
Warning: Variant 487 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
147/165  [('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696884_LOC115697762_LOC115696986.hmp snp_cluster_LOC115696884_LOC115697762_LOC115696986.map > snp_cluster_LOC115696884_LOC115697762_LOC115696986.ped'
Warning: Variant 223 triallelic; setting rarest alleles missing.
Warning: Variant 252 triallelic; setting rarest alleles missing.
Warning: Variant 267 triallelic; setting rarest alleles missing.
Warning: Variant 276 triallelic; setting rarest alleles missing.
Warning: Variant 286 triallelic; setting rarest alleles missing.
Warning: Variant 368 triallelic; setting rarest alleles missing.
Warning: Variant 391 triallelic; setting rarest alleles missing.
Warning: Variant 455 triallelic; setting rarest alleles missing.
Warning: Variant 475 triallelic; setting rarest alleles missing.
Warning: Variant 535 triallelic; setting rarest alleles missing.
Warning: Variant 604 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
148/165  [('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696884_LOC115697762_LOC115697126.hmp snp_cluster_LOC115696884_LOC115697762_LOC115697126.map > snp_cluster_LOC115696884_LOC115697762_LOC115697126.ped'
Warning: Variant 223 triallelic; setting rarest alleles missing.
Warning: Variant 252 triallelic; setting rarest alleles missing.
Warning: Variant 267 triallelic; setting rarest alleles missing.
Warning: Variant 276 triallelic; setting rarest alleles missing.
Warning: Variant 286 triallelic; setting rarest alleles missing.
Warning: Variant 368 triallelic; setting rarest alleles missing.
Warning: Variant 391 triallelic; setting rarest alleles missing.
Warning: Variant 455 triallelic; setting rarest alleles missing.
Warning: Variant 475 triallelic; setting rarest alleles missing.
Warning: Variant 513 triallelic; setting rarest alleles missing.
Warning: Variant 514 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
149/165  [('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696884_LOC115697762_LOC115697019.hmp snp_cluster_LOC115696884_LOC115697762_LOC115697019.map > snp_cluster_LOC115696884_LOC115697762_LOC115697019.ped'
Warning: Variant 223 triallelic; setting rarest alleles missing.
Warning: Variant 252 triallelic; setting rarest alleles missing.
Warning: Variant 267 triallelic; setting rarest alleles missing.
Warning: Variant 276 triallelic; setting rarest alleles missing.
Warning: Variant 286 triallelic; setting rarest alleles missing.
Warning: Variant 368 triallelic; setting rarest alleles missing.
Warning: Variant 391 triallelic; setting rarest alleles missing.
Warning: Variant 455 triallelic; setting rarest alleles missing.
Warning: Variant 475 triallelic; setting rarest alleles missing.
Warning: Variant 549 quadallelic; setting rarest alleles missing.
Warning: Variant 581 triallelic; setting rarest alleles missing.
Warning: Variant 598 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.8547917524226172  Normalized VI=0.6220387028480509'
150/165  [('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696884_LOC115696987_LOC115696986.hmp snp_cluster_LOC115696884_LOC115696987_LOC115696986.map > snp_cluster_LOC115696884_LOC115696987_LOC115696986.ped'
Warning: Variant 207 triallelic; setting rarest alleles missing.
Warning: Variant 304 triallelic; setting rarest alleles missing.
Warning: Variant 373 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8162415166341106  Normalized VI=0.988978217634648'
151/165  [('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696884_LOC115696987_LOC115697126.hmp snp_cluster_LOC115696884_LOC115696987_LOC115697126.map > snp_cluster_LOC115696884_LOC115696987_LOC115697126.ped'
Warning: Variant 207 triallelic; setting rarest alleles missing.
Warning: Variant 282 triallelic; setting rarest alleles missing.
Warning: Variant 283 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8777784073370816  Normalized VI=0.9945413167421732'
152/165  [('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696884_LOC115696987_LOC115697019.hmp snp_cluster_LOC115696884_LOC115696987_LOC115697019.map > snp_cluster_LOC115696884_LOC115696987_LOC115697019.ped'
Warning: Variant 207 triallelic; setting rarest alleles missing.
Warning: Variant 318 quadallelic; setting rarest alleles missing.
Warning: Variant 350 triallelic; setting rarest alleles missing.
Warning: Variant 367 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.086069973143601  Normalized VI=0.727816423672658'
153/165  [('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696884_LOC115696986_LOC115697126.hmp snp_cluster_LOC115696884_LOC115696986_LOC115697126.map > snp_cluster_LOC115696884_LOC115696986_LOC115697126.ped'
Warning: Variant 255 triallelic; setting rarest alleles missing.
Warning: Variant 324 triallelic; setting rarest alleles missing.
Warning: Variant 392 triallelic; setting rarest alleles missing.
Warning: Variant 393 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.860096152813166  Normalized VI=0.9924582072316522'
154/165  [('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696884_LOC115696986_LOC115697019.hmp snp_cluster_LOC115696884_LOC115696986_LOC115697019.map > snp_cluster_LOC115696884_LOC115696986_LOC115697019.ped'
Warning: Variant 255 triallelic; setting rarest alleles missing.
Warning: Variant 324 triallelic; setting rarest alleles missing.
Warning: Variant 428 quadallelic; setting rarest alleles missing.
Warning: Variant 460 triallelic; setting rarest alleles missing.
Warning: Variant 477 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.802407341921462  Normalized VI=0.9871748993262272'
155/165  [('NC_044378.1', '29635083', '29636878', 'LOC115696884'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696884_LOC115697126_LOC115697019.hmp snp_cluster_LOC115696884_LOC115697126_LOC115697019.map > snp_cluster_LOC115696884_LOC115697126_LOC115697019.ped'
Warning: Variant 233 triallelic; setting rarest alleles missing.
Warning: Variant 234 triallelic; setting rarest alleles missing.
Warning: Variant 341 quadallelic; setting rarest alleles missing.
Warning: Variant 373 triallelic; setting rarest alleles missing.
Warning: Variant 390 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.9698437088952239  Normalized VI=0.6799622681151731'
156/165  [('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697762_LOC115696987_LOC115696986.hmp snp_cluster_LOC115697762_LOC115696987_LOC115696986.map > snp_cluster_LOC115697762_LOC115696987_LOC115696986.ped'
Warning: Variant 17 triallelic; setting rarest alleles missing.
Warning: Variant 46 triallelic; setting rarest alleles missing.
Warning: Variant 61 triallelic; setting rarest alleles missing.
Warning: Variant 70 triallelic; setting rarest alleles missing.
Warning: Variant 80 triallelic; setting rarest alleles missing.
Warning: Variant 162 triallelic; setting rarest alleles missing.
Warning: Variant 185 triallelic; setting rarest alleles missing.
Warning: Variant 249 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 281 triallelic; setting rarest alleles missing.
Warning: Variant 378 triallelic; setting rarest alleles missing.
Warning: Variant 447 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
157/165  [('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697762_LOC115696987_LOC115697126.hmp snp_cluster_LOC115697762_LOC115696987_LOC115697126.map > snp_cluster_LOC115697762_LOC115696987_LOC115697126.ped'
Warning: Variant 17 triallelic; setting rarest alleles missing.
Warning: Variant 46 triallelic; setting rarest alleles missing.
Warning: Variant 61 triallelic; setting rarest alleles missing.
Warning: Variant 70 triallelic; setting rarest alleles missing.
Warning: Variant 80 triallelic; setting rarest alleles missing.
Warning: Variant 162 triallelic; setting rarest alleles missing.
Warning: Variant 185 triallelic; setting rarest alleles missing.
Warning: Variant 249 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 281 triallelic; setting rarest alleles missing.
Warning: Variant 356 triallelic; setting rarest alleles missing.
Warning: Variant 357 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
158/165  [('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697762_LOC115696987_LOC115697019.hmp snp_cluster_LOC115697762_LOC115696987_LOC115697019.map > snp_cluster_LOC115697762_LOC115696987_LOC115697019.ped'
Warning: Variant 17 triallelic; setting rarest alleles missing.
Warning: Variant 46 triallelic; setting rarest alleles missing.
Warning: Variant 61 triallelic; setting rarest alleles missing.
Warning: Variant 70 triallelic; setting rarest alleles missing.
Warning: Variant 80 triallelic; setting rarest alleles missing.
Warning: Variant 162 triallelic; setting rarest alleles missing.
Warning: Variant 185 triallelic; setting rarest alleles missing.
Warning: Variant 249 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 281 triallelic; setting rarest alleles missing.
Warning: Variant 392 quadallelic; setting rarest alleles missing.
Warning: Variant 424 triallelic; setting rarest alleles missing.
Warning: Variant 441 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
159/165  [('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697762_LOC115696986_LOC115697126.hmp snp_cluster_LOC115697762_LOC115696986_LOC115697126.map > snp_cluster_LOC115697762_LOC115696986_LOC115697126.ped'
Warning: Variant 17 triallelic; setting rarest alleles missing.
Warning: Variant 46 triallelic; setting rarest alleles missing.
Warning: Variant 61 triallelic; setting rarest alleles missing.
Warning: Variant 70 triallelic; setting rarest alleles missing.
Warning: Variant 80 triallelic; setting rarest alleles missing.
Warning: Variant 162 triallelic; setting rarest alleles missing.
Warning: Variant 185 triallelic; setting rarest alleles missing.
Warning: Variant 249 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 329 triallelic; setting rarest alleles missing.
Warning: Variant 398 triallelic; setting rarest alleles missing.
Warning: Variant 466 triallelic; setting rarest alleles missing.
Warning: Variant 467 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
160/165  [('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697762_LOC115696986_LOC115697019.hmp snp_cluster_LOC115697762_LOC115696986_LOC115697019.map > snp_cluster_LOC115697762_LOC115696986_LOC115697019.ped'
Warning: Variant 17 triallelic; setting rarest alleles missing.
Warning: Variant 46 triallelic; setting rarest alleles missing.
Warning: Variant 61 triallelic; setting rarest alleles missing.
Warning: Variant 70 triallelic; setting rarest alleles missing.
Warning: Variant 80 triallelic; setting rarest alleles missing.
Warning: Variant 162 triallelic; setting rarest alleles missing.
Warning: Variant 185 triallelic; setting rarest alleles missing.
Warning: Variant 249 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 329 triallelic; setting rarest alleles missing.
Warning: Variant 398 triallelic; setting rarest alleles missing.
Warning: Variant 502 quadallelic; setting rarest alleles missing.
Warning: Variant 534 triallelic; setting rarest alleles missing.
Warning: Variant 551 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
161/165  [('NC_044378.1', '30980884', '30982768', 'LOC115697762'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115697762_LOC115697126_LOC115697019.hmp snp_cluster_LOC115697762_LOC115697126_LOC115697019.map > snp_cluster_LOC115697762_LOC115697126_LOC115697019.ped'
Warning: Variant 17 triallelic; setting rarest alleles missing.
Warning: Variant 46 triallelic; setting rarest alleles missing.
Warning: Variant 61 triallelic; setting rarest alleles missing.
Warning: Variant 70 triallelic; setting rarest alleles missing.
Warning: Variant 80 triallelic; setting rarest alleles missing.
Warning: Variant 162 triallelic; setting rarest alleles missing.
Warning: Variant 185 triallelic; setting rarest alleles missing.
Warning: Variant 249 triallelic; setting rarest alleles missing.
Warning: Variant 269 triallelic; setting rarest alleles missing.
Warning: Variant 307 triallelic; setting rarest alleles missing.
Warning: Variant 308 triallelic; setting rarest alleles missing.
Warning: Variant 415 quadallelic; setting rarest alleles missing.
Warning: Variant 447 triallelic; setting rarest alleles missing.
Warning: Variant 464 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=0.6534187172841676  Normalized VI=0.5335581095538917'
162/165  [('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696987_LOC115696986_LOC115697126.hmp snp_cluster_LOC115696987_LOC115696986_LOC115697126.map > snp_cluster_LOC115696987_LOC115696986_LOC115697126.ped'
Warning: Variant 1 triallelic; setting rarest alleles missing.
Warning: Variant 98 triallelic; setting rarest alleles missing.
Warning: Variant 167 triallelic; setting rarest alleles missing.
Warning: Variant 235 triallelic; setting rarest alleles missing.
Warning: Variant 236 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.9122154127168802  Normalized VI=0.9987344691696657'
163/165  [('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696987_LOC115696986_LOC115697019.hmp snp_cluster_LOC115696987_LOC115696986_LOC115697019.map > snp_cluster_LOC115696987_LOC115696986_LOC115697019.ped'
Warning: Variant 1 triallelic; setting rarest alleles missing.
Warning: Variant 98 triallelic; setting rarest alleles missing.
Warning: Variant 167 triallelic; setting rarest alleles missing.
Warning: Variant 271 quadallelic; setting rarest alleles missing.
Warning: Variant 303 triallelic; setting rarest alleles missing.
Warning: Variant 320 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8291508103636218  Normalized VI=0.9906126940411427'
164/165  [('NC_044378.1', '34047624', '34048440', 'LOC115696987'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696987_LOC115697126_LOC115697019.hmp snp_cluster_LOC115696987_LOC115697126_LOC115697019.map > snp_cluster_LOC115696987_LOC115697126_LOC115697019.ped'
Warning: Variant 1 triallelic; setting rarest alleles missing.
Warning: Variant 76 triallelic; setting rarest alleles missing.
Warning: Variant 77 triallelic; setting rarest alleles missing.
Warning: Variant 184 quadallelic; setting rarest alleles missing.
Warning: Variant 216 triallelic; setting rarest alleles missing.
Warning: Variant 233 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8642509055695178  Normalized VI=0.9909264782077022'
165/165  [('NC_044378.1', '34056091', '34061726', 'LOC115696986'), ('NC_044378.1', '34132843', '34134661', 'LOC115697126'), ('NC_044378.1', '61398236', '61400085', 'LOC115697019')]

'common samples  130'
'python HapMap_to_PLINK.py snp_cluster_LOC115696986_LOC115697126_LOC115697019.hmp snp_cluster_LOC115696986_LOC115697126_LOC115697019.map > snp_cluster_LOC115696986_LOC115697126_LOC115697019.ped'
Warning: Variant 49 triallelic; setting rarest alleles missing.
Warning: Variant 118 triallelic; setting rarest alleles missing.
Warning: Variant 186 triallelic; setting rarest alleles missing.
Warning: Variant 187 triallelic; setting rarest alleles missing.
Warning: Variant 294 quadallelic; setting rarest alleles missing.
Warning: Variant 326 triallelic; setting rarest alleles missing.
Warning: Variant 343 triallelic; setting rarest alleles missing.
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'Variation of Information=1.8494338585322114  Normalized VI=0.9910610499945303'
LOC115717841_LOC115718836_LOC115720716

LOC115717841_LOC115718836_LOC115697880

LOC115717841_LOC115718836_LOC115696909

LOC115717841_LOC115718836_LOC115696884

LOC115717841_LOC115718836_LOC115697762

LOC115717841_LOC115718836_LOC115696987

LOC115717841_LOC115718836_LOC115696986

LOC115717841_LOC115718836_LOC115697126

LOC115717841_LOC115718836_LOC115697019

LOC115717841_LOC115720716_LOC115697880

LOC115717841_LOC115720716_LOC115696909

LOC115717841_LOC115720716_LOC115696884

LOC115717841_LOC115720716_LOC115697762

LOC115717841_LOC115720716_LOC115696987

LOC115717841_LOC115720716_LOC115696986

LOC115717841_LOC115720716_LOC115697126

LOC115717841_LOC115720716_LOC115697019

LOC115717841_LOC115697880_LOC115696909

LOC115717841_LOC115697880_LOC115696884

LOC115717841_LOC115697880_LOC115697762

LOC115717841_LOC115697880_LOC115696987

LOC115717841_LOC115697880_LOC115696986

LOC115717841_LOC115697880_LOC115697126

LOC115717841_LOC115697880_LOC115697019

LOC115717841_LOC115696909_LOC115696884

LOC115717841_LOC115696909_LOC115697762

LOC115717841_LOC115696909_LOC115696987

LOC115717841_LOC115696909_LOC115696986

LOC115717841_LOC115696909_LOC115697126

LOC115717841_LOC115696909_LOC115697019

LOC115717841_LOC115696884_LOC115697762

LOC115717841_LOC115696884_LOC115696987

LOC115717841_LOC115696884_LOC115696986

LOC115717841_LOC115696884_LOC115697126

LOC115717841_LOC115696884_LOC115697019

LOC115717841_LOC115697762_LOC115696987

LOC115717841_LOC115697762_LOC115696986

LOC115717841_LOC115697762_LOC115697126

LOC115717841_LOC115697762_LOC115697019

LOC115717841_LOC115696987_LOC115696986

LOC115717841_LOC115696987_LOC115697126

LOC115717841_LOC115696987_LOC115697019

LOC115717841_LOC115696986_LOC115697126

LOC115717841_LOC115696986_LOC115697019

LOC115717841_LOC115697126_LOC115697019

LOC115718836_LOC115720716_LOC115697880

LOC115718836_LOC115720716_LOC115696909

LOC115718836_LOC115720716_LOC115696884

LOC115718836_LOC115720716_LOC115697762

LOC115718836_LOC115720716_LOC115696987

LOC115718836_LOC115720716_LOC115696986

LOC115718836_LOC115720716_LOC115697126

LOC115718836_LOC115720716_LOC115697019

LOC115718836_LOC115697880_LOC115696909

LOC115718836_LOC115697880_LOC115696884

LOC115718836_LOC115697880_LOC115697762

LOC115718836_LOC115697880_LOC115696987

LOC115718836_LOC115697880_LOC115696986

LOC115718836_LOC115697880_LOC115697126

LOC115718836_LOC115697880_LOC115697019

LOC115718836_LOC115696909_LOC115696884

LOC115718836_LOC115696909_LOC115697762

LOC115718836_LOC115696909_LOC115696987

LOC115718836_LOC115696909_LOC115696986

LOC115718836_LOC115696909_LOC115697126

LOC115718836_LOC115696909_LOC115697019

LOC115718836_LOC115696884_LOC115697762

LOC115718836_LOC115696884_LOC115696987

LOC115718836_LOC115696884_LOC115696986

LOC115718836_LOC115696884_LOC115697126

LOC115718836_LOC115696884_LOC115697019

LOC115718836_LOC115697762_LOC115696987

LOC115718836_LOC115697762_LOC115696986

LOC115718836_LOC115697762_LOC115697126

LOC115718836_LOC115697762_LOC115697019

LOC115718836_LOC115696987_LOC115696986

LOC115718836_LOC115696987_LOC115697126

LOC115718836_LOC115696987_LOC115697019

LOC115718836_LOC115696986_LOC115697126

LOC115718836_LOC115696986_LOC115697019

LOC115718836_LOC115697126_LOC115697019

LOC115720716_LOC115697880_LOC115696909

LOC115720716_LOC115697880_LOC115696884

LOC115720716_LOC115697880_LOC115697762

LOC115720716_LOC115697880_LOC115696987

LOC115720716_LOC115697880_LOC115696986

LOC115720716_LOC115697880_LOC115697126

LOC115720716_LOC115697880_LOC115697019

LOC115720716_LOC115696909_LOC115696884

LOC115720716_LOC115696909_LOC115697762

LOC115720716_LOC115696909_LOC115696987

LOC115720716_LOC115696909_LOC115696986

LOC115720716_LOC115696909_LOC115697126

LOC115720716_LOC115696909_LOC115697019

LOC115720716_LOC115696884_LOC115697762

LOC115720716_LOC115696884_LOC115696987

LOC115720716_LOC115696884_LOC115696986

LOC115720716_LOC115696884_LOC115697126

LOC115720716_LOC115696884_LOC115697019

LOC115720716_LOC115697762_LOC115696987

LOC115720716_LOC115697762_LOC115696986

LOC115720716_LOC115697762_LOC115697126

LOC115720716_LOC115697762_LOC115697019

LOC115720716_LOC115696987_LOC115696986

LOC115720716_LOC115696987_LOC115697126

LOC115720716_LOC115696987_LOC115697019

LOC115720716_LOC115696986_LOC115697126

LOC115720716_LOC115696986_LOC115697019

LOC115720716_LOC115697126_LOC115697019

LOC115697880_LOC115696909_LOC115696884

LOC115697880_LOC115696909_LOC115697762

LOC115697880_LOC115696909_LOC115696987

LOC115697880_LOC115696909_LOC115696986

LOC115697880_LOC115696909_LOC115697126

LOC115697880_LOC115696909_LOC115697019

LOC115697880_LOC115696884_LOC115697762

LOC115697880_LOC115696884_LOC115696987

LOC115697880_LOC115696884_LOC115696986

LOC115697880_LOC115696884_LOC115697126

LOC115697880_LOC115696884_LOC115697019

LOC115697880_LOC115697762_LOC115696987

LOC115697880_LOC115697762_LOC115696986

LOC115697880_LOC115697762_LOC115697126

LOC115697880_LOC115697762_LOC115697019

LOC115697880_LOC115696987_LOC115696986

LOC115697880_LOC115696987_LOC115697126

LOC115697880_LOC115696987_LOC115697019

LOC115697880_LOC115696986_LOC115697126

LOC115697880_LOC115696986_LOC115697019

LOC115697880_LOC115697126_LOC115697019

LOC115696909_LOC115696884_LOC115697762

LOC115696909_LOC115696884_LOC115696987

LOC115696909_LOC115696884_LOC115696986

LOC115696909_LOC115696884_LOC115697126

LOC115696909_LOC115696884_LOC115697019

LOC115696909_LOC115697762_LOC115696987

LOC115696909_LOC115697762_LOC115696986

LOC115696909_LOC115697762_LOC115697126

LOC115696909_LOC115697762_LOC115697019

LOC115696909_LOC115696987_LOC115696986

LOC115696909_LOC115696987_LOC115697126

LOC115696909_LOC115696987_LOC115697019

LOC115696909_LOC115696986_LOC115697126

LOC115696909_LOC115696986_LOC115697019

LOC115696909_LOC115697126_LOC115697019

LOC115696884_LOC115697762_LOC115696987

LOC115696884_LOC115697762_LOC115696986

LOC115696884_LOC115697762_LOC115697126

LOC115696884_LOC115697762_LOC115697019

LOC115696884_LOC115696987_LOC115696986

LOC115696884_LOC115696987_LOC115697126

LOC115696884_LOC115696987_LOC115697019

LOC115696884_LOC115696986_LOC115697126

LOC115696884_LOC115696986_LOC115697019

LOC115696884_LOC115697126_LOC115697019

LOC115697762_LOC115696987_LOC115696986

LOC115697762_LOC115696987_LOC115697126

LOC115697762_LOC115696987_LOC115697019

LOC115697762_LOC115696986_LOC115697126

LOC115697762_LOC115696986_LOC115697019

LOC115697762_LOC115697126_LOC115697019

LOC115696987_LOC115696986_LOC115697126

LOC115696987_LOC115696986_LOC115697019

LOC115696987_LOC115697126_LOC115697019

LOC115696986_LOC115697126_LOC115697019
region VI Normalized VI Jaccard
Loading... (need help?)

3-gene combination was also then run, and combine the results from 1-gene, 2-gene, and 3-gene. Then sort by VI for the best and worst combination

In [19]:
pdvi_all=pd.concat([pdvi1, pdvi2, pdvi3])
display(pdvi_all)
region VI Normalized VI Jaccard
Loading... (need help?)

Using plink (filtered SNPs) The worst is LOC115720716_LOC115696909 with Normalized VI of 0.99992, and the best are LOC115718836_LOC115720716_LOC115697762 and LOC115718836_LOC115697762_LOC115697019 with NVI of 0.503647. Show the plots for these combinations

Using live SNP query (all SNPs) The worst is LOC115696909_LOC115696986 with Normalized VI of 0.999989, and the best are LOC115718836_LOC115696884 and LOC115696884_LOC115697126 with NVI of 0.117162. Show the plots for these combinations

In [22]:
# filtered
#combinations=['LOC115720716_LOC115696909', 'LOC115718836_LOC115720716_LOC115697762', 'LOC115718836_LOC115697762_LOC115697019']

#live
combinations=['LOC115696909_LOC115696986', 'LOC115718836_LOC115696884', 'LOC115696884_LOC115697126']

vi_jaccard_scores=dict()
for reg in combinations:
    genes=reg.split("_")
    
    print(reg)
    display(df_raw[df_raw['name'].isin(genes)])
    
    #gene1range=gene2range[genes[0]]
    #urlloc='https://icgrc.info/api/user/variant/' + gene1range[0] + ':' + gene1range[1] + '-' + gene1range[2] + '?snpds=7ds&ref=cs10' 
    #reg=gene1range[0] + '_' + gene1range[1] + '_' + gene1range[2]  
    #plink_extract=[]
    #for combs in genes:
    #    plink_extract.append(gene2range[combs])
    #print(plink_extract)
    
    regions=[]
    for g in genes:
        gene1range=gene2range[g]
        regions.append(gene1range[0] + ':' + gene1range[1] + '-' + gene1range[2])
    regions=",".join(regions)
    
    urlloc='https://icgrc.info/api/user/variant/' + regions + '?snpds=7ds&ref=cs10' 
    df_snp= read_url(urlloc,reg,requery=REQUERY_URL)


    #vi_jaccard_scores[reg]=do_clustering(df_snp,reg,'cultivar_group',convert_group=convert_group,K=2,heatmap=True,plink_file=PLINKFILE,plink_extract=plink_extract)
    vi_jaccard_scores[reg]=do_clustering(df_snp,reg,'cultivar_group',convert_group=convert_group,K=2,heatmap=True)    
    

LOC115696909_LOC115696986
name contig fmin fmax strand gb_keyword go_term interpro_value
Loading... (need help?)
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'bedtools getfasta -fi /home/lmansu10/data/reference/cs10refseq.fna -bed cluster_LOC115696909_LOC115696986.btbed > cluster_LOC115696909_LOC115696986.bed.ref'
plink --bfile cluster_LOC115696909_LOC115696986 --recode tab --out cluster_LOC115696909_LOC115696986_ped --allow-extra-chr

'cluster_LOC115696909_LOC115696986_ped.ped.tsv  generated'
python draw_tree_matrix.py cluster_LOC115696909_LOC115696986_ped.ped.tsv cluster_LOC115696909_LOC115696986.newick
Click here to download: type_snpseektree_cluster_LOC115696909_LOC115696986.newick.rename.nwk.rr.png
No description has been provided for this image 
'Variation of Information=1.876809108851948  Normalized VI=0.9999890667707702'
LOC115718836_LOC115696884
name contig fmin fmax strand gb_keyword go_term interpro_value
Loading... (need help?)
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'bedtools getfasta -fi /home/lmansu10/data/reference/cs10refseq.fna -bed cluster_LOC115718836_LOC115696884.btbed > cluster_LOC115718836_LOC115696884.bed.ref'
plink --bfile cluster_LOC115718836_LOC115696884 --recode tab --out cluster_LOC115718836_LOC115696884_ped --allow-extra-chr

'cluster_LOC115718836_LOC115696884_ped.ped.tsv  generated'
python draw_tree_matrix.py cluster_LOC115718836_LOC115696884_ped.ped.tsv cluster_LOC115718836_LOC115696884.newick
Click here to download: type_snpseektree_cluster_LOC115718836_LOC115696884.newick.rename.nwk.rr.png
No description has been provided for this image 
'Variation of Information=0.11507166270421601  Normalized VI=0.11716232178800956'
LOC115696884_LOC115697126
name contig fmin fmax strand gb_keyword go_term interpro_value
Loading... (need help?)
Loading required package: MASS
Loading required package: abind
Loading required package: epitools
Loading required package: meta
Loading 'meta' package (version 6.5-0).
Type 'help(meta)' for a brief overview.
Readers of 'Meta-Analysis with R (Use R!)' should install
older version of 'meta' package: https://tinyurl.com/dt4y5drs

'bedtools getfasta -fi /home/lmansu10/data/reference/cs10refseq.fna -bed cluster_LOC115696884_LOC115697126.btbed > cluster_LOC115696884_LOC115697126.bed.ref'
plink --bfile cluster_LOC115696884_LOC115697126 --recode tab --out cluster_LOC115696884_LOC115697126_ped --allow-extra-chr

'cluster_LOC115696884_LOC115697126_ped.ped.tsv  generated'
python draw_tree_matrix.py cluster_LOC115696884_LOC115697126_ped.ped.tsv cluster_LOC115696884_LOC115697126.newick
Click here to download: type_snpseektree_cluster_LOC115696884_LOC115697126.newick.rename.nwk.rr.png
No description has been provided for this image 
'Variation of Information=0.11507166270421601  Normalized VI=0.11716232178800956'
In [ ]: