1KG VCF 파일의 일부 (22번 염색체에서 5천개 변이 추철)
%matplotlib inline
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
!head -n 19 only_rs_22-5000.vcf
##fileformat=VCFv4.0 ##filedat=20101112 ##datarelease=20100804 ##samples=629 ##description="Where BI calls are present, genotypes and alleles are from BI. In there absence, UM genotypes are used. If neither are available, no genotype information is present and the alleles are from the NCBI calls." ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)"> ##FORMAT=<ID=GL,Number=3,Type=Float,Description="Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic"> ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=GD,Number=1,Type=Float,Description="Genotype dosage. Expected count of non-ref alleles [0,2]"> ##FORMAT=<ID=OG,Number=1,Type=String,Description="Original Genotype input to Beagle"> ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> ##INFO=<ID=CB,Number=.,Type=String,Description="List of centres that called, UM (University of Michigan), BI (Broad Institute), BC (Boston College), NCBI"> ##INFO=<ID=EUR_R2,Number=1,Type=Float,Description="R2 From Beagle based on European Samples"> ##INFO=<ID=AFR_R2,Number=1,Type=Float,Description="R2 From Beagle based on AFRICAN Samples"> ##INFO=<ID=ASN_R2,Number=1,Type=Float,Description="R2 From Beagle based on Asian Samples"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00098 HG00100 HG00106 HG00112 HG00114 HG00116 HG00117 HG00118 HG00119 HG00120 HG00122 HG00123 HG00124 HG00126 HG00131 HG00141 HG00142 HG00143 HG00144 HG00145 HG00146 HG00147 HG00148 HG00149 HG00150 HG00151 HG00152 HG00153 HG00156 HG00158 HG00159 HG00160 HG00171 HG00173 HG00174 HG00176 HG00177 HG00178 HG00179 HG00180 HG00181 HG00182 HG00183 HG00185 HG00186 HG00187 HG00188 HG00189 HG00190 HG00231 HG00239 HG00242 HG00243 HG00244 HG00245 HG00247 HG00258 HG00262 HG00264 HG00265 HG00266 HG00267 HG00269 HG00270 HG00272 HG00306 HG00308 HG00311 HG00312 HG00357 HG00361 HG00366 HG00367 HG00368 HG00369 HG00372 HG00373 HG00377 HG00380 HG00403 HG00404 HG00406 HG00407 HG00445 HG00446 HG00452 HG00457 HG00553 HG00554 HG00559 HG00560 HG00565 HG00566 HG00577 HG00578 HG00592 HG00593 HG00596 HG00610 HG00611 HG00625 HG00626 HG00628 HG00629 HG00634 HG00635 HG00637 HG00638 HG00640 NA06984 NA06985 NA06986 NA06989 NA06994 NA07000 NA07037 NA07048 NA07051 NA07056 NA07346 NA07347 NA07357 NA10847 NA10851 NA11829 NA11830 NA11831 NA11832 NA11840 NA11843 NA11881 NA11892 NA11893 NA11894 NA11918 NA11919 NA11920 NA11930 NA11931 NA11932 NA11933 NA11992 NA11993 NA11994 NA11995 NA12003 NA12004 NA12005 NA12006 NA12043 NA12044 NA12045 NA12046 NA12058 NA12144 NA12154 NA12155 NA12156 NA12249 NA12272 NA12273 NA12275 NA12287 NA12340 NA12341 NA12342 NA12347 NA12348 NA12383 NA12399 NA12400 NA12413 NA12414 NA12489 NA12546 NA12716 NA12717 NA12718 NA12749 NA12750 NA12751 NA12761 NA12762 NA12763 NA12775 NA12776 NA12777 NA12778 NA12812 NA12813 NA12814 NA12815 NA12828 NA12830 NA12872 NA12873 NA12874 NA12889 NA12890 NA18486 NA18487 NA18489 NA18498 NA18499 NA18501 NA18502 NA18504 NA18505 NA18507 NA18508 NA18510 NA18511 NA18516 NA18517 NA18519 NA18520 NA18522 NA18523 NA18525 NA18526 NA18527 NA18532 NA18535 NA18537 NA18538 NA18539 NA18541 NA18542 NA18545 NA18547 NA18550 NA18552 NA18553 NA18555 NA18558 NA18560 NA18561 NA18562 NA18563 NA18564 NA18565 NA18566 NA18567 NA18570 NA18571 NA18572 NA18573 NA18574 NA18576 NA18577 NA18579 NA18582 NA18592 NA18593 NA18603 NA18605 NA18608 NA18609 NA18611 NA18612 NA18614 NA18615 NA18616 NA18617 NA18618 NA18619 NA18620 NA18621 NA18622 NA18623 NA18624 NA18625 NA18626 NA18627 NA18628 NA18630 NA18631 NA18632 NA18633 NA18634 NA18636 NA18638 NA18640 NA18642 NA18643 NA18745 NA18853 NA18856 NA18858 NA18861 NA18867 NA18868 NA18870 NA18871 NA18873 NA18874 NA18907 NA18908 NA18909 NA18910 NA18912 NA18916 NA18940 NA18941 NA18942 NA18943 NA18944 NA18945 NA18947 NA18948 NA18949 NA18950 NA18951 NA18952 NA18953 NA18955 NA18956 NA18959 NA18960 NA18961 NA18963 NA18964 NA18965 NA18967 NA18968 NA18970 NA18971 NA18972 NA18973 NA18974 NA18975 NA18976 NA18977 NA18979 NA18980 NA18981 NA18982 NA18983 NA18984 NA18985 NA18986 NA18987 NA18988 NA18989 NA18990 NA18997 NA18999 NA19000 NA19001 NA19002 NA19003 NA19004 NA19005 NA19007 NA19009 NA19010 NA19012 NA19027 NA19044 NA19054 NA19055 NA19056 NA19057 NA19058 NA19059 NA19060 NA19062 NA19063 NA19064 NA19065 NA19066 NA19067 NA19068 NA19070 NA19072 NA19074 NA19075 NA19076 NA19077 NA19078 NA19079 NA19082 NA19083 NA19084 NA19085 NA19086 NA19087 NA19088 NA19093 NA19098 NA19099 NA19102 NA19107 NA19108 NA19113 NA19114 NA19116 NA19119 NA19129 NA19130 NA19131 NA19137 NA19138 NA19141 NA19143 NA19144 NA19147 NA19152 NA19153 NA19159 NA19160 NA19171 NA19172 NA19184 NA19189 NA19190 NA19200 NA19201 NA19204 NA19206 NA19207 NA19209 NA19210 NA19213 NA19225 NA19235 NA19236 NA19247 NA19248 NA19256 NA19257 NA19311 NA19312 NA19313 NA19314 NA19332 NA19334 NA19338 NA19346 NA19347 NA19350 NA19355 NA19359 NA19360 NA19371 NA19372 NA19375 NA19376 NA19377 NA19379 NA19381 NA19382 NA19383 NA19384 NA19385 NA19390 NA19391 NA19393 NA19394 NA19395 NA19397 NA19398 NA19399 NA19401 NA19404 NA19428 NA19429 NA19434 NA19435 NA19436 NA19437 NA19438 NA19439 NA19440 NA19443 NA19444 NA19445 NA19446 NA19448 NA19449 NA19451 NA19452 NA19453 NA19455 NA19456 NA19457 NA19461 NA19462 NA19463 NA19466 NA19467 NA19469 NA19471 NA19472 NA19473 NA19474 NA19625 NA19648 NA19649 NA19651 NA19652 NA19654 NA19655 NA19658 NA19660 NA19661 NA19678 NA19684 NA19685 NA19700 NA19701 NA19703 NA19704 NA19707 NA19712 NA19713 NA19720 NA19722 NA19723 NA19725 NA19726 NA19818 NA19819 NA19834 NA19835 NA19900 NA19901 NA19904 NA19908 NA19909 NA19914 NA19916 NA19917 NA19920 NA19921 NA19982 NA20414 NA20502 NA20505 NA20508 NA20509 NA20510 NA20512 NA20515 NA20516 NA20517 NA20518 NA20519 NA20520 NA20521 NA20522 NA20524 NA20525 NA20526 NA20527 NA20528 NA20529 NA20530 NA20531 NA20532 NA20533 NA20534 NA20535 NA20536 NA20537 NA20538 NA20539 NA20540 NA20541 NA20542 NA20543 NA20544 NA20581 NA20582 NA20585 NA20586 NA20588 NA20589 NA20752 NA20753 NA20754 NA20755 NA20756 NA20757 NA20758 NA20759 NA20760 NA20761 NA20765 NA20769 NA20770 NA20771 NA20772 NA20773 NA20774 NA20775 NA20778 NA20783 NA20785 NA20786 NA20787 NA20790 NA20792 NA20795 NA20796 NA20797 NA20798 NA20799 NA20800 NA20801 NA20802 NA20803 NA20804 NA20805 NA20806 NA20807 NA20808 NA20809 NA20810 NA20811 NA20812 NA20813 NA20814 NA20815 NA20816 NA20818 NA20819 NA20826 NA20828
df = pd.read_table('only_rs_22-5000.vcf', skiprows=18)
df
#CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | FORMAT | HG00098 | ... | NA20811 | NA20812 | NA20813 | NA20814 | NA20815 | NA20816 | NA20818 | NA20819 | NA20826 | NA20828 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | 22 | 50328528 | rs116643340 | G | C | . | PASS | DP=269;AF=0.010;CB=BI,NCBI;AFR_R2=0.516 | GT:AD:DP:GD:GL:GQ:OG | ./.:.:.:.:.,.,.:.:./. | ... | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. |
1 | 22 | 50328670 | rs114196268 | G | A | . | PASS | DP=1089;AF=0.007;CB=UM,BI,BC,NCBI;AFR_R2=0.465 | GT:AD:DP:GD:GL:GQ:OG | ./.:.:.:.:.,.,.:.:./. | ... | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. |
2 | 22 | 50328731 | rs28608875 | C | T | . | PASS | DP=907;AF=0.055;CB=UM,BI,BC,NCBI;EUR_R2=0.751;... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:19.48:./. | ... | 0|0:3,0:3:.:-0.00,-0.90,-10.06:31.02:./. | 0|0:7,0:5:.:-0.01,-1.51,-14.93:25.32:./. | 0|0:2,0:2:.:-0.00,-0.60,-6.66:25.58:./. | 0|0:1,0:1:.:-0.00,-0.30,-3.47:22.60:./. | 0|0:3,0:3:.:-0.00,-0.90,-9.31:28.57:./. | 1|0:3,0:3:.:-0.00,-0.90,-10.19:3.84:0/0 | 0|0:3,0:3:.:-0.00,-0.90,-9.86:28.57:./. | 0|1:2,0:2:.:-0.00,-0.60,-7.19:5.60:0/0 | 0|0:4,0:3:.:-0.00,-0.90,-10.16:18.81:./. | 0|0:5,0:3:.:-0.00,-0.91,-9.26:31.14:./. |
3 | 22 | 50329119 | rs56008904 | C | T | . | PASS | DP=141;AF=0.390;CB=BI,BC;EUR_R2=0.145;AFR_R2=0... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:3.49:./. | ... | 1|0:.:.:.:.,.,.:3.36:./. | 0|0:1,0:1:.:-0.00,-0.30,-3.17:3.87:./. | 0|0:.:.:.:.,.,.:3.54:./. | 0|0:.:.:.:.,.,.:3.54:./. | 0|0:1,0:1:.:-0.00,-0.30,-2.37:5.94:./. | 1|0:0,1:1:.:-3.87,-0.30,-0.00:4.71:1/1 | 0|0:.:.:.:.,.,.:3.54:./. | 1|1:.:.:.:.,.,.:1.71:./. | 1|0:.:.:.:.,.,.:3.22:./. | 1|0:.:.:.:.,.,.:3.36:./. |
4 | 22 | 50329830 | rs79860705 | G | A | . | PASS | DP=373;AF=0.107;CB=UM,BI,BC,NCBI;EUR_R2=0.507 | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:9.26:./. | ... | 0|0:1,0:1:.:-0.00,-0.30,-3.47:11.92:./. | 1|0:1,2:2:.:-6.43,-0.60,-0.00:6.99:1/1 | 0|0:1,0:1:.:-0.00,-0.30,-2.50:12.12:./. | 0|0:.:.:.:.,.,.:9.26:./. | 0|0:1,0:1:.:-0.00,-0.30,-2.80:12.12:./. | 0|0:3,0:3:.:-0.00,-0.90,-9.43:5.77:./. | 0|0:.:.:.:.,.,.:9.26:./. | 0|1:.:.:.:.,.,.:5.52:./. | 0|0:3,1:3:.:-0.00,-0.91,-8.99:9.32:./. | 0|0:1,0:1:.:-0.00,-0.30,-3.30:11.93:./. |
5 | 22 | 50330186 | rs73444002 | G | T | . | PASS | DP=1024;AF=0.026;CB=UM,BI,BC,NCBI;EUR_R2=0.498... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:27.01:./. | ... | 0|0:2,0:2:.:-0.00,-0.60,-6.86:19.92:./. | 0|0:2,0:2:.:-0.00,-0.60,-6.01:41.55:./. | 0|0:3,0:3:.:-0.00,-0.90,-10.67:42.22:./. | 0|0:7,0:5:.:-0.01,-1.51,-14.76:46.99:./. | 0|0:3,0:3:.:-0.00,-0.90,-10.26:41.55:./. | 0|0:2,0:2:.:-0.00,-0.60,-6.90:35.23:./. | 0|0:.:.:.:.,.,.:32.76:./. | 0|0:2,0:1:.:-0.00,-0.30,-3.50:15.52:./. | 0|0:5,0:5:.:-0.00,-1.51,-17.40:27.64:./. | 0|0:1,0:1:.:-0.00,-0.30,-3.56:16.98:./. |
6 | 22 | 50330345 | rs28652639 | G | A | . | PASS | DP=1477;AF=0.016;CB=UM,BI,BC,NCBI;EUR_R2=0.605 | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:11.33:./. | ... | 0|0:3,0:3:.:-0.00,-0.90,-10.19:18.58:./. | 0|0:3,0:2:.:-0.00,-0.60,-5.89:20.27:./. | 0|0:3,0:3:.:-0.00,-0.90,-10.99:20.27:./. | 0|0:.:.:.:.,.,.:11.47:./. | 1|0:2,3:5:.:-9.59,-1.51,-6.07:60:./. | 0|0:6,0:6:.:-0.00,-1.81,-21.59:32.22:./. | 0|0:.:.:.:.,.,.:11.44:./. | 0|0:1,0:1:.:-0.00,-0.30,-3.70:13.38:./. | 0|0:8,0:6:.:-0.01,-1.81,-18.99:26.82:./. | 0|0:4,0:2:.:-0.00,-0.60,-7.09:15.63:./. |
7 | 22 | 50330546 | rs28516848 | T | G | . | PASS | DP=1517;AF=0.061;CB=UM,BI,BC,NCBI;EUR_R2=0.773... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:21.35:./. | ... | 0|0:.:.:.:.,.,.:21.73:./. | 0|0:6,0:6:.:-0.00,-1.81,-19.50:45.23:./. | 0|0:5,0:5:.:-0.00,-1.51,-18.62:39.59:./. | 0|0:6,0:6:.:-0.00,-1.81,-21.26:43.01:./. | 0|0:3,0:3:.:-0.00,-0.90,-10.43:33.87:./. | 0|0:5,0:5:.:-0.00,-1.51,-17.46:43.01:./. | 0|0:.:.:.:.,.,.:24.67:./. | 1|0:1,1:2:.:-2.80,-0.60,-2.94:43.98:./. | 0|0:3,0:3:.:-0.00,-0.90,-10.93:36.20:./. | 0|0:3,0:2:.:-0.00,-0.60,-7.49:30.22:./. |
8 | 22 | 50331032 | rs115322211 | G | A | . | PASS | DP=1465;AF=0.013;CB=UM,BI,BC,NCBI;AFR_R2=0.711 | GT:AD:DP:GD:GL:GQ:OG | ./.:.:.:.:.,.,.:.:./. | ... | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. |
9 | 22 | 50331164 | rs28690400 | T | C | . | PASS | DP=1538;AF=0.299;CB=UM,BI,BC,NCBI;EUR_R2=0.929... | GT:AD:DP:GD:GL:GQ:OG | 0|0:1,0:1:.:-0.00,-0.30,-3.46:23.76:./. | ... | 0|0:2,0:2:.:-0.00,-0.60,-6.43:24.96:./. | 1|0:4,2:4:.:-2.80,-1.21,-10.48:50:./. | 0|0:9,0:9:.:-0.01,-2.72,-31.86:60:./. | 0|0:2,0:2:.:-0.00,-0.61,-6.82:50:./. | 0|0:4,0:4:.:-0.00,-1.21,-14.35:60:./. | 1|0:3,3:5:.:-5.97,-1.51,-11.20:60:./. | 0|0:1,0:1:.:-0.00,-0.30,-3.57:43.98:./. | 1|1:0,3:3:.:-8.76,-0.91,-0.01:37.21:./. | 1|0:3,1:4:.:-3.20,-1.21,-11.00:22.73:./. | 0|0:8,0:6:.:-0.00,-1.81,-22.28:42.22:./. |
10 | 22 | 50331300 | rs73891184 | T | C | . | PASS | DP=1799;AF=0.020;CB=UM,BI,BC,NCBI;AFR_R2=0.759 | GT:AD:DP:GD:GL:GQ:OG | ./.:.:.:.:.,.,.:.:./. | ... | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. |
11 | 22 | 50331475 | rs76433322 | A | G | . | PASS | DP=2162;AF=0.009;CB=UM,BI,BC,NCBI;AFR_R2=0.732 | GT:AD:DP:GD:GL:GQ:OG | ./.:.:.:.:.,.,.:.:./. | ... | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. |
12 | 22 | 50331622 | rs28393180 | C | T | . | PASS | DP=1952;AF=0.052;CB=UM,BI,BC,NCBI;EUR_R2=0.68;... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:24.96:./. | ... | 0|0:6,0:6:.:-0.01,-1.81,-17.47:60:./. | 0|0:13,0:11:.:-0.02,-3.33,-30.65:60:./. | 0|0:16,0:16:.:-0.02,-4.83,-49.96:60:./. | 0|0:3,0:2:.:-0.00,-0.60,-5.66:50:./. | 0|0:8,0:7:.:-0.01,-2.11,-20.85:43.01:./. | 0|0:1,0:1:.:-0.00,-0.30,-3.10:60:./. | 0|0:1,0:1:.:-0.00,-0.30,-2.90:28.96:./. | 0|0:3,0:3:.:-0.00,-0.90,-9.33:60:./. | 0|0:8,0:7:.:-0.01,-2.11,-22.39:60:./. | 0|0:6,0:4:.:-0.00,-1.21,-12.77:60:./. |
13 | 22 | 50332005 | rs28460675 | G | T | . | PASS | DP=2228;AF=0.144;CB=UM,BI,BC,NCBI;EUR_R2=0.918... | GT:AD:DP:GD:GL:GQ:OG | 0|0:1,0:1:.:-0.00,-0.30,-2.40:17.77:./. | ... | 1|0:1,5:5:.:-13.57,-1.51,-2.80:50:./. | 0|0:6,0:4:.:-0.01,-1.21,-11.77:50:./. | 0|0:18,0:17:.:-0.02,-5.13,-53.88:60:./. | 0|0:6,0:4:.:-0.00,-1.21,-11.66:46.99:./. | 0|0:6,0:5:.:-0.01,-1.51,-16.23:26.78:./. | 0|0:5,0:5:.:-0.01,-1.51,-15.63:60:./. | 0|0:2,0:1:.:-0.00,-0.30,-3.06:28.54:./. | 1|0:4,1:5:.:-3.90,-1.51,-12.42:43.01:./. | 0|0:6,0:6:.:-0.01,-1.81,-17.97:46.99:./. | 1|0:5,2:6:.:-3.90,-1.81,-15.46:39.21:./. |
14 | 22 | 50332022 | rs28470489 | T | A | . | PASS | DP=2210;AF=0.438;CB=UM,BI,BC,NCBI;EUR_R2=0.972... | GT:AD:DP:GD:GL:GQ:OG | 0|0:1,0:1:.:-0.00,-0.30,-2.94:16.89:./. | ... | 1|0:2,3:5:.:-10.04,-1.51,-6.48:60:./. | 1|0:4,3:6:.:-6.94,-1.81,-13.38:60:./. | 0|0:17,0:16:.:-0.01,-4.82,-58.10:60:./. | 0|0:5,0:5:.:-0.00,-1.51,-18.06:45.23:./. | 0|0:5,0:5:.:-0.00,-1.51,-19.09:50:./. | 1|0:4,5:8:.:-14.36,-2.41,-13.48:60:./. | 0|0:1,0:1:.:-0.00,-0.30,-3.70:27.93:./. | 1|1:0,7:6:.:-20.45,-1.81,-0.00:60:./. | 1|0:2,3:5:.:-10.48,-1.51,-6.60:60:./. | 1|0:6,3:9:.:-11.04,-2.71,-20.50:60:./. |
15 | 22 | 50332097 | rs77228592 | C | T | . | PASS | DP=2104;AF=0.020;CB=UM,BI,BC,NCBI;EUR_R2=0.483... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:21.60:./. | ... | 0|0:2,0:2:.:-0.00,-0.60,-6.06:30.56:./. | 0|0:10,0:7:.:-0.01,-2.11,-21.06:45.23:./. | 0|0:19,0:19:.:-0.02,-5.73,-60.41:60:./. | 0|0:10,0:8:.:-0.01,-2.41,-26.40:45.23:./. | 0|0:4,0:2:.:-0.00,-0.60,-5.46:27.93:./. | 0|0:4,0:4:.:-0.00,-1.21,-12.20:36.58:./. | 0|0:.:.:.:.,.,.:21.56:./. | 0|0:8,0:6:.:-0.01,-1.81,-17.99:60:./. | 0|0:4,0:3:.:-0.00,-0.90,-9.76:33.57:./. | 0|0:5,0:5:.:-0.00,-1.51,-16.43:39.59:./. |
16 | 22 | 50332242 | rs28451805 | A | G | . | PASS | DP=3101;AF=0.426;CB=UM,BI,BC,NCBI;EUR_R2=0.969... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:17.48:./. | ... | 1|0:7,3:9:.:-8.00,-2.72,-23.94:60:./. | 1|0:7,2:9:.:-6.07,-2.72,-23.15:60:./. | 0|0:31,0:30:.:-0.02,-9.04,-109.61:60:./. | 0|0:11,0:11:.:-0.01,-3.32,-40.19:60:./. | 0|0:18,0:16:.:-0.02,-4.83,-57.14:60:./. | 1|0:7,5:12:.:-18.26,-3.62,-24.95:60:./. | 0|0:7,0:7:.:-0.01,-2.12,-22.43:50:./. | 1|1:0,4:4:.:-14.33,-1.20,-0.00:33.28:./. | 1|0:13,6:19:.:-23.89,-5.73,-47.23:60:./. | 1|0:11,2:12:.:-7.08,-3.62,-35.26:60:./. |
17 | 22 | 50332324 | rs28523661 | T | C | . | PASS | DP=3435;AF=0.587;CB=UM,BI,BC,NCBI;EUR_R2=0.755... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:4.64:./. | ... | 1|1:0,15:14:.:-45.50,-4.22,-0.02:60:./. | 1|0:14,13:24:.:-32.97,-7.24,-45.55:60:./. | 0|1:25,24:44:.:-64.95,-13.26,-90.40:60:./. | 0|0:10,0:9:.:-0.01,-2.72,-32.25:30.71:./. | 0|0:17,0:17:.:-0.02,-5.13,-60.28:60:./. | 1|1:0,12:10:.:-31.71,-3.01,-0.01:23.48:./. | 0|1:3,2:4:.:-2.67,-1.21,-10.78:11.43:./. | 1|1:0,2:2:.:-7.36,-0.60,-0.00:18.29:./. | 1|0:19,12:28:.:-40.16,-8.44,-62.12:60:./. | 1|0:12,3:15:.:-10.84,-4.52,-45.63:60:./. |
18 | 22 | 50332377 | rs114353012 | C | T | . | PASS | DP=3208;AF=0.003;CB=UM,BC,NCBI | GT:AD:DP:GD:GL:GQ:OG | ./.:.:.:.:.,.,.:.:./. | ... | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. |
19 | 22 | 50332472 | rs115364094 | C | G | . | PASS | DP=3376;AF=0.003;CB=UM,BI,BC,NCBI;AFR_R2=0.824 | GT:AD:DP:GD:GL:GQ:OG | ./.:.:.:.:.,.,.:.:./. | ... | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. |
20 | 22 | 50333130 | rs77002698 | G | A | . | PASS | DP=1951;AF=0.081;CB=UM,BI,BC,NCBI;EUR_R2=0.886... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:30.97:./. | ... | 0|0:3,0:2:.:-0.00,-0.60,-6.16:40.46:./. | 1|0:6,3:6:.:-7.14,-1.81,-12.28:60:./. | 0|0:10,0:10:.:-0.01,-3.01,-32.30:60:./. | 0|0:8,0:5:.:-0.00,-1.51,-16.60:46.99:./. | 0|0:4,0:3:.:-0.00,-0.91,-9.36:41.55:./. | 1|0:7,5:8:.:-3.76,-2.41,-22.63:28.66:./. | 0|0:2,0:2:.:-0.00,-0.60,-6.06:37.45:./. | 0|1:2,2:2:.:-7.23,-0.60,-0.00:60:1/1 | 1|0:7,3:7:.:-11.48,-2.11,-11.99:60:./. | 0|0:9,0:7:.:-0.01,-2.11,-21.89:60:./. |
21 | 22 | 50333253 | rs116837852 | G | A | . | PASS | DP=2488;AF=0.010;CB=UM,BI,BC,NCBI;AFR_R2=0.822 | GT:AD:DP:GD:GL:GQ:OG | ./.:.:.:.:.,.,.:.:./. | ... | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. |
22 | 22 | 50333415 | rs4073387 | G | A | . | PASS | DP=2144;AF=0.087;CB=UM,BI,BC,NCBI;EUR_R2=0.967... | GT:AD:DP:GD:GL:GQ:OG | 0|0:1,0:1:.:-0.00,-0.30,-2.80:26.09:./. | ... | 0|0:4,0:3:.:-0.00,-0.90,-9.03:34.81:./. | 1|0:4,4:6:.:-14.77,-1.81,-5.67:60:./. | 0|0:6,0:6:.:-0.01,-1.81,-18.69:40.97:./. | 0|0:4,0:3:.:-0.00,-0.90,-9.66:32.29:./. | 0|0:6,0:6:.:-0.01,-1.81,-17.65:41.55:./. | 1|0:6,3:9:.:-10.60,-2.72,-17.67:60:./. | 0|0:4,0:4:.:-0.01,-1.21,-11.86:35.09:./. | 0|1:1,0:1:.:-0.00,-0.30,-2.80:26.13:0/0 | 1|0:4,3:7:.:-11.69,-2.11,-12.10:60:./. | 0|0:6,0:5:.:-0.00,-1.51,-16.25:41.55:./. |
23 | 22 | 50333697 | rs4073388 | C | G | . | PASS | DP=1957;AF=0.073;CB=UM,BI,BC,NCBI;EUR_R2=0.885... | GT:AD:DP:GD:GL:GQ:OG | 0|0:1,0:1:.:-0.00,-0.30,-4.05:23.48:./. | ... | 0|0:4,0:3:.:-0.00,-0.90,-11.94:31.87:./. | 1|0:5,2:5:.:-4.20,-1.51,-14.08:40.46:./. | 0|0:10,0:8:.:-0.01,-2.42,-31.35:43.98:./. | 0|0:2,0:1:.:-0.00,-0.30,-3.89:23.68:./. | 0|0:1,0:1:.:-0.00,-0.30,-3.89:23.97:./. | 1|0:2,3:4:.:-7.20,-1.21,-7.09:60:./. | 0|0:2,0:1:.:-0.00,-0.30,-3.69:23.29:./. | 0|1:.:.:.:.,.,.:11.50:./. | 1|0:1,3:3:.:-7.84,-0.91,-3.79:50:./. | 0|0:5,0:4:.:-0.00,-1.21,-15.77:35.69:./. |
24 | 22 | 50333748 | rs114900897 | C | T | . | PASS | DP=2417;AF=0.022;CB=UM,BI,BC,NCBI;AFR_R2=0.818 | GT:AD:DP:GD:GL:GQ:OG | ./.:.:.:.:.,.,.:.:./. | ... | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. |
25 | 22 | 50334208 | rs4073885 | C | T | . | PASS | DP=2555;AF=0.022;CB=UM,BI,BC,NCBI;AFR_R2=0.75 | GT:AD:DP:GD:GL:GQ:OG | ./.:.:.:.:.,.,.:.:./. | ... | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. |
26 | 22 | 50334409 | rs28376035 | A | G | . | PASS | DP=2092;AF=0.059;CB=UM,BI;EUR_R2=0.815;AFR_R2=... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:31.43:./. | ... | 0|0:5,0:2:.:-0.00,-0.60,-8.23:40.46:./. | 1|0:5,4:6:.:-5.50,-1.81,-13.56:46.99:./. | 0|0:6,0:3:.:-0.01,-0.91,-9.48:40.46:./. | 0|0:9,0:5:.:-0.00,-1.51,-19.71:46.99:./. | 0|0:8,0:5:.:-0.00,-1.51,-18.92:46.99:./. | 1|0:7,2:4:.:-5.99,-1.21,-7.33:60:./. | 0|0:7,0:4:.:-0.01,-1.21,-12.22:43.01:./. | 0|1:7,0:1:.:-0.00,-0.30,-3.97:7.52:0/0 | 1|0:3,5:5:.:-9.76,-1.51,-7.94:60:./. | 0|0:11,0:7:.:-0.01,-2.11,-26.55:60:./. |
27 | 22 | 50334415 | rs28405006 | C | T | . | PASS | DP=2200;AF=0.055;CB=UM,BI,BC;AFR_R2=0.651 | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:60:./. | ... | 0|0:4,0:2:.:-0.00,-0.60,-6.74:60:./. | 0|0:10,0:6:.:-0.01,-1.81,-18.07:60:./. | 0|0:7,0:5:.:-0.01,-1.51,-15.08:60:./. | 0|0:10,0:6:.:-0.00,-1.81,-19.77:60:./. | 0|0:7,0:3:.:-0.00,-0.90,-9.83:60:./. | 0|0:11,0:5:.:-0.00,-1.51,-16.20:60:./. | 0|0:6,0:3:.:-0.01,-0.91,-8.59:60:./. | 0|0:6,0:3:.:-0.00,-0.91,-9.43:60:./. | 0|0:9,0:6:.:-0.01,-1.81,-18.67:60:./. | 0|0:12,0:8:.:-0.01,-2.41,-25.90:60:./. |
28 | 22 | 50334443 | rs28612446 | T | C | . | PASS | DP=2398;AF=0.069;CB=UM,BI,BC,NCBI;EUR_R2=0.907... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:28.39:./. | ... | 0|0:7,0:7:.:-0.00,-2.11,-26.13:50:./. | 1|0:7,5:8:.:-11.93,-2.42,-13.84:60:./. | 0|0:7,1:6:.:-0.00,-1.81,-22.49:46.99:./. | 0|0:11,0:11:.:-0.01,-3.32,-40.97:60:./. | 0|0:5,0:3:.:-0.00,-0.90,-10.89:37.21:./. | 1|0:8,5:10:.:-9.36,-3.01,-26.04:60:./. | 0|0:7,0:5:.:-0.00,-1.51,-18.51:43.01:./. | 0|1:4,2:4:.:-2.57,-1.21,-11.88:23.38:./. | 1|0:3,3:5:.:-9.29,-1.51,-7.43:60:./. | 0|0:8,0:5:.:-0.00,-1.51,-19.78:46.99:./. |
29 | 22 | 50334680 | rs62234028 | A | G | . | PASS | DP=2743;AF=0.099;CB=UM,BI,BC,NCBI;EUR_R2=0.98;... | GT:AD:DP:GD:GL:GQ:OG | 0|0:2,0:2:.:-0.00,-0.60,-8.02:39.21:./. | ... | 0|0:5,0:5:.:-0.00,-1.51,-18.40:60:./. | 1|0:1,5:5:.:-10.79,-1.51,-3.68:60:./. | 0|0:11,0:9:.:-0.00,-2.71,-33.87:60:./. | 0|0:5,0:5:.:-0.00,-1.51,-19.51:50:./. | 0|0:3,0:3:.:-0.00,-0.90,-11.89:45.23:./. | 1|0:7,3:9:.:-6.00,-2.71,-25.63:60:./. | 0|0:1,0:1:.:-0.00,-0.30,-2.86:38.24:./. | 0|1:0,1:1:.:-2.77,-0.30,-0.00:42.22:1/1 | 1|0:3,4:6:.:-9.73,-1.81,-11.39:60:./. | 0|0:2,0:2:.:-0.00,-0.60,-7.92:43.98:./. |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
4970 | 22 | 51217134 | rs117417021 | A | G | . | PASS | DP=1636;AF=0.080;CB=BI,BC;EUR_R2=0.423;AFR_R2=... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:6.73:./. | ... | 0|0:.:.:.:.,.,.:9.80:./. | 0|0:4,1:3:.:-0.00,-0.91,-10.29:22.85:./. | 0|0:.:.:.:.,.,.:8.07:./. | 0|0:3,0:3:.:-0.00,-0.90,-11.08:20.32:./. | 0|0:4,0:3:.:-0.00,-0.90,-11.29:22.06:./. | 0|0:.:.:.:.,.,.:5.15:./. | 0|0:.:.:.:.,.,.:6.92:./. | 0|0:2,0:2:.:-0.00,-0.60,-7.62:15.65:./. | 0|0:4,0:4:.:-0.00,-1.20,-16.16:24.93:./. | 0|0:6,0:6:.:-0.00,-1.81,-23.76:32.01:./. |
4971 | 22 | 51217954 | rs9616974 | G | A | . | PASS | DP=2572;AF=0.066;CB=UM,BI;EUR_R2=0.925;AFR_R2=... | GT:AD:DP:GD:GL:GQ:OG | 0|0:2,0:2:.:-0.00,-0.60,-6.04:10.47:./. | ... | 0|0:8,0:3:.:-0.00,-0.90,-11.16:40.97:./. | 0|0:4,0:1:.:-0.00,-0.30,-3.20:34.32:./. | 0|1:2,1:2:.:-2.87,-0.61,-3.47:34.81:./. | 0|0:5,0:1:.:-0.00,-0.30,-4.00:34.56:./. | 0|0:3,0:3:.:-0.00,-0.90,-9.81:40.46:./. | 0|0:12,0:4:.:-0.01,-1.21,-12.57:45.23:./. | 0|0:2,0:3:.:-2.80,-3.31,-8.58:26.29:./. | 0|0:2,0:1:.:-0.00,-0.30,-3.80:34.69:./. | 0|0:10,0:7:.:-0.00,-2.11,-25.06:50:./. | 0|0:.:.:.:.,.,.:31.14:./. |
4972 | 22 | 51218224 | rs9616975 | C | A | . | PASS | DP=2741;AF=0.050;CB=UM,BI,BC,NCBI;EUR_R2=0.699... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:12.69:./. | ... | 0|0:10,0:4:.:-0.00,-1.21,-13.47:43.98:./. | 0|0:9,0:4:.:-0.00,-1.21,-12.66:43.01:./. | 0|1:4,3:4:.:-5.23,-1.21,-6.86:60:./. | 0|0:.:.:.:.,.,.:31.74:./. | 0|0:.:.:.:.,.,.:31.49:./. | 0|0:7,0:3:.:-0.00,-0.90,-9.92:40:./. | 0|0:.:.:.:.,.,.:27.19:./. | 0|0:.:.:.:.,.,.:30.71:./. | 0|0:11,0:4:.:-0.00,-1.21,-12.40:43.98:./. | 0|0:.:.:.:.,.,.:30.86:./. |
4973 | 22 | 51218615 | rs117845379 | T | A | . | PASS | DP=2071;AF=0.067;CB=UM,BI,BC,NCBI;EUR_R2=0.765... | GT:AD:DP:GD:GL:GQ:OG | 0|0:1,0:1:.:-0.00,-0.30,-4.00:11.69:./. | ... | 0|0:10,0:9:.:-0.01,-2.71,-29.75:60:./. | 0|0:7,0:6:.:-0.00,-1.81,-20.37:50:./. | 0|1:6,1:7:.:-3.70,-2.11,-20.97:21.16:./. | 0|0:2,0:2:.:-0.00,-0.60,-7.10:36.99:./. | 0|0:3,0:3:.:-0.00,-0.91,-9.40:38.24:./. | 0|0:10,0:9:.:-0.01,-2.71,-30.25:60:./. | 0|0:7,0:5:.:-0.01,-1.51,-15.97:35.23:./. | 0|0:3,0:3:.:-0.00,-0.90,-9.98:40.46:./. | 0|0:3,0:3:.:-0.00,-0.90,-10.44:40.46:./. | 0|0:5,0:5:.:-0.01,-1.51,-16.19:46.99:./. |
4974 | 22 | 51218957 | rs116323389 | A | G | . | PASS | DP=3192;AF=0.015;CB=UM,BI,BC,NCBI;AFR_R2=0.867 | GT:AD:DP:GD:GL:GQ:OG | 0|0:1,0:1:.:-0.00,-0.30,-4.07:33.57:./. | ... | 0|0:4,0:4:.:-0.00,-1.20,-15.63:37.45:./. | 0|0:4,0:4:.:-0.00,-1.21,-13.55:38.86:./. | 0|0:4,0:4:.:-0.00,-1.21,-13.56:40.97:./. | 0|0:8,0:8:.:-0.00,-2.41,-30.60:50:./. | 0|0:7,0:7:.:-0.00,-2.11,-26.21:46.99:./. | 0|0:6,0:5:.:-0.00,-1.51,-18.50:41.55:./. | 0|0:1,0:1:.:-0.00,-0.30,-3.76:32.52:./. | 0|0:4,0:4:.:-0.00,-1.21,-13.35:38.24:./. | 0|0:10,0:10:.:-0.00,-3.01,-37.71:60:./. | 0|0:8,0:7:.:-0.00,-2.11,-26.22:46.99:./. |
4975 | 22 | 51219006 | rs28729663 | G | A | . | PASS | DP=3270;AF=0.200;CB=UM,BI,BC,NCBI;EUR_R2=0.871... | GT:AD:DP:GD:GL:GQ:OG | 0|1:0,1:1:.:-3.77,-0.30,-0.00:7.51:1/1 | ... | 0|0:8,0:7:.:-0.00,-2.11,-22.66:35.69:./. | 0|0:6,0:5:.:-0.01,-1.51,-14.95:30:./. | 0|1:3,2:5:.:-7.21,-1.51,-10.29:60:./. | 0|0:8,0:10:.:-6.24,-8.71,-30.87:40:./. | 0|0:4,0:4:.:-0.00,-1.21,-12.30:26.99:./. | 0|0:6,0:5:.:-0.00,-1.51,-15.80:29.96:./. | 1|0:2,1:3:.:-3.87,-0.90,-6.49:38.54:./. | 0|0:3,0:3:.:-0.00,-0.90,-9.73:23.74:./. | 0|0:9,0:9:.:-0.01,-2.71,-29.33:42.22:./. | 0|0:5,0:5:.:-0.01,-1.51,-15.33:30.71:./. |
4976 | 22 | 51219216 | rs6010087 | G | A | . | PASS | DP=3115;AF=0.002;CB=UM,BI,NCBI;AFR_R2=0.794 | GT:AD:DP:GD:GL:GQ:OG | ./.:.:.:.:.,.,.:.:./. | ... | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. |
4977 | 22 | 51219382 | rs118066233 | G | A | . | PASS | DP=2889;AF=0.000;CB=BI,BC,NCBI;AFR_R2=0.957 | GT:AD:DP:GD:GL:GQ:OG | 0|0:1,0:1:.:-0.00,-0.30,-3.50:60:./. | ... | 0|0:8,0:8:.:-0.00,-2.41,-26.36:60:./. | 0|0:7,0:6:.:-0.01,-1.81,-17.14:60:./. | 0|0:9,0:9:.:-0.00,-2.71,-29.83:60:./. | 0|0:2,0:1:.:-0.00,-0.30,-3.30:60:./. | 0|0:3,0:3:.:-0.00,-0.90,-10.36:60:./. | 0|0:1,0:1:.:-0.00,-0.30,-3.40:60:./. | 0|0:3,0:2:.:-0.00,-0.60,-6.34:60:./. | 0|0:2,0:2:.:-0.00,-0.60,-7.06:60:./. | 0|0:4,0:4:.:-0.00,-1.20,-15.28:60:./. | 0|0:3,0:2:.:-0.00,-0.60,-6.44:60:./. |
4978 | 22 | 51219387 | rs9616832 | T | C | . | PASS | DP=2796;AF=0.069;CB=UM,BI,BC,NCBI;EUR_R2=0.952... | GT:AD:DP:GD:GL:GQ:OG | 0|0:1,0:1:.:-0.00,-0.30,-4.06:10.25:./. | ... | 0|0:10,0:9:.:-0.00,-2.71,-34.55:60:./. | 0|0:7,0:6:.:-0.00,-1.81,-21.99:50:./. | 0|1:7,2:7:.:-3.17,-2.11,-23.27:46.99:./. | 0|0:2,0:1:.:-0.00,-0.30,-3.86:34.69:./. | 0|0:3,0:3:.:-0.00,-0.90,-11.58:40.46:./. | 0|0:1,0:1:.:-0.00,-0.30,-3.86:38.24:./. | 0|0:3,0:3:.:-0.00,-0.90,-11.69:26.80:./. | 0|0:3,0:2:.:-0.00,-0.60,-7.12:37.96:./. | 0|0:4,0:4:.:-0.00,-1.20,-15.82:43.98:./. | 0|0:3,0:3:.:-0.00,-0.90,-11.40:39.59:./. |
4979 | 22 | 51220441 | rs76759269 | T | C | . | PASS | DP=1857;AF=1.000;CB=UM,BI,BC | GT:AD:DP:GD:GL:GQ:OG | 1|1:0,1:1:.:-2.80,-0.30,-0.00:36.58:./. | ... | 1|1:0,2:2:.:-5.96,-0.60,-0.00:38.24:./. | 1|1:0,7:5:.:-14.73,-1.51,-0.01:46.99:./. | 1|1:0,13:9:.:-27.58,-2.71,-0.01:60:./. | 1|1:0,8:3:.:-8.83,-0.90,-0.00:40.97:./. | 1|1:0,5:4:.:-11.73,-1.21,-0.01:43.98:./. | 1|1:0,6:6:.:-18.17,-1.81,-0.01:50:./. | 1|1:0,1:1:.:-3.07,-0.30,-0.00:36.20:./. | 1|1:0,7:5:.:-15.10,-1.51,-0.00:46.99:./. | 1|1:0,4:4:.:-12.56,-4.54,-3.95:37.96:./. | 1|1:0,4:3:.:-8.93,-0.91,-0.00:40.97:./. |
4980 | 22 | 51220848 | rs9616981 | C | A | . | PASS | DP=3053;AF=0.126;CB=UM,BI,BC;EUR_R2=0.607;AFR_... | GT:AD:DP:GD:GL:GQ:OG | 0|0:1,2:1:.:-0.00,-0.30,-3.66:10.88:./. | ... | 0|0:14,1:14:.:-0.01,-4.22,-44.95:60:./. | 0|0:7,0:7:.:-0.01,-2.11,-20.53:31.80:./. | 0|0:5,1:5:.:-0.00,-1.51,-16.56:18.25:./. | 0|0:2,0:1:.:-0.00,-0.30,-3.46:12.84:./. | 0|0:6,0:5:.:-0.00,-1.51,-16.37:25.21:./. | 0|0:17,1:17:.:-0.01,-5.12,-55.22:60:./. | 0|0:5,0:4:.:-0.00,-1.21,-11.96:20.55:./. | 0|0:2,0:2:.:-0.00,-0.60,-6.56:16.09:./. | 0|0:12,0:12:.:-0.00,-3.61,-41.70:46.99:./. | 0|0:9,2:9:.:-0.01,-2.71,-30.09:37.96:./. |
4981 | 22 | 51220938 | rs78802599 | A | G | . | PASS | DP=4787;AF=0.220;CB=BI,BC,NCBI;EUR_R2=0.667;AF... | GT:AD:DP:GD:GL:GQ:OG | 0|0:1,1:1:.:-0.00,-0.30,-4.07:6.93:./. | ... | 0|1:5,1:6:.:-3.40,-1.81,-19.62:12.98:./. | 0|0:6,1:6:.:-0.00,-1.81,-20.77:21.40:./. | 0|0:11,2:11:.:-3.30,-3.32,-37.84:3.99:./. | 1|0:4,2:3:.:-3.50,-0.90,-8.03:22.92:./. | 0|0:13,0:13:.:-0.01,-3.92,-48.33:60:./. | 0|0:13,3:13:.:-3.17,-3.92,-44.70:11.14:./. | 0|0:3,0:3:.:-0.00,-0.90,-11.18:12.39:./. | 0|0:2,0:2:.:-0.00,-0.60,-7.53:9.72:./. | 0|0:9,0:9:.:-0.00,-2.71,-35.56:30.41:./. | 0|0:6,1:6:.:-0.00,-1.81,-24.48:21.42:./. |
4982 | 22 | 51221731 | rs115055839 | T | C | . | PASS | DP=2518;AF=0.059;CB=UM,BI,BC,NCBI;EUR_R2=0.807... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:10.76:./. | ... | 0|0:4,0:4:.:-0.01,-1.21,-14.17:31.74:./. | 0|0:8,0:8:.:-0.01,-2.41,-27.82:45.23:./. | 0|1:7,11:17:.:-32.13,-5.12,-26.47:60:./. | 0|0:2,0:1:.:-0.00,-0.30,-3.17:19.80:./. | 0|0:7,0:7:.:-0.00,-2.11,-26.33:42.22:./. | 0|0:5,0:5:.:-0.00,-1.51,-18.14:36.78:./. | 0|0:9,0:9:.:-0.01,-2.72,-31.78:45.23:./. | 0|0:7,0:5:.:-0.01,-1.51,-16.91:34.32:./. | 0|0:12,0:12:.:-0.01,-3.62,-44.65:60:./. | 0|0:10,0:9:.:-0.01,-2.72,-32.28:50:./. |
4983 | 22 | 51222052 | rs2879915 | G | A | . | PASS | DP=979;AF=0.190;CB=UM,BI,BC,NCBI;EUR_R2=0.314;... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:3.02:./. | ... | 1|1:2,4:3:.:-9.18,-0.91,-0.01:4:./. | 0|0:3,0:1:.:-0.00,-0.30,-3.07:5.90:./. | 0|1:2,2:2:.:-3.76,-0.60,-2.70:26.09:./. | 1|0:2,5:2:.:-7.52,-0.60,-0.00:3.70:1/1 | 0|0:2,0:2:.:-0.00,-0.60,-6.46:8.15:./. | 1|1:0,6:4:.:-14.32,-1.21,-0.00:6.43:./. | 0|0:.:.:.:.,.,.:3.07:./. | 0|1:5,1:5:.:-3.36,-1.51,-12.50:17.28:./. | 1|0:0,1:1:.:-3.86,-0.30,-0.00:5.98:1/1 | 0|0:10,0:8:.:-0.01,-2.41,-24.49:25.70:./. |
4984 | 22 | 51222100 | rs114553188 | G | T | . | PASS | DP=840;AF=0.082;CB=UM,BI;EUR_R2=0.393;AFR_R2=0... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:9.42:./. | ... | 0|0:.:.:.:.,.,.:9.82:./. | 0|0:4,0:3:.:-0.00,-0.90,-9.57:18.88:./. | 0|0:5,0:4:.:-0.01,-1.21,-11.76:21.34:./. | 0|0:4,0:1:.:-0.00,-0.30,-2.70:13.09:./. | 0|0:2,0:2:.:-0.00,-0.60,-7.11:15.88:./. | 0|0:3,0:3:.:-0.00,-0.90,-8.86:18.88:./. | 1|0:.:.:.:.,.,.:1.94:./. | 0|0:3,1:2:.:-0.00,-0.60,-7.21:15.75:./. | 0|0:2,0:2:.:-0.00,-0.60,-6.06:15.99:./. | 0|0:5,0:4:.:-0.01,-1.21,-12.22:21.89:./. |
4985 | 22 | 51223848 | rs2519470 | C | G | . | PASS | DP=2632;AF=0.020;CB=BI,BC;AFR_R2=0.782 | GT:AD:DP:GD:GL:GQ:OG | 0|0:2,0:1:.:-0.00,-0.30,-4.49:60:./. | ... | 0|0:6,1:5:.:-0.01,-1.51,-19.73:60:./. | 0|0:8,0:7:.:-0.01,-2.11,-27.90:60:./. | 0|0:9,0:7:.:-0.01,-2.11,-28.36:60:./. | 0|0:6,0:5:.:-0.00,-1.51,-20.18:60:./. | 0|0:6,0:5:.:-0.00,-1.51,-20.12:60:./. | 0|0:7,0:6:.:-0.00,-1.81,-25.01:60:./. | 0|0:7,0:5:.:-0.01,-1.51,-19.17:60:./. | 0|0:5,0:5:.:-0.01,-1.51,-18.37:60:./. | 0|0:12,0:12:.:-0.01,-3.62,-49.18:60:./. | 0|0:3,0:3:.:-0.00,-0.91,-11.78:60:./. |
4986 | 22 | 51224208 | rs116656403 | G | A | . | PASS | DP=3100;AF=0.024;CB=UM,BI,NCBI;AFR_R2=0.936 | GT:AD:DP:GD:GL:GQ:OG | 0|0:2,0:2:.:-0.00,-0.60,-7.06:37.45:./. | ... | 0|0:3,0:3:.:-0.00,-0.90,-9.43:40.46:./. | 0|0:9,0:9:.:-0.01,-2.72,-28.91:60:./. | 0|0:11,0:11:.:-0.01,-3.32,-36.33:60:./. | 0|0:4,0:2:.:-0.00,-0.60,-6.46:37.45:./. | 0|0:5,0:4:.:-0.00,-1.21,-13.36:43.98:./. | 0|0:14,0:13:.:-0.02,-3.92,-40.44:60:./. | 0|0:4,0:2:.:-0.00,-0.60,-6.64:37.45:./. | 0|0:1,0:1:.:-0.00,-0.30,-3.40:34.56:./. | 0|0:8,0:8:.:-0.00,-2.41,-26.71:60:./. | 0|0:6,0:5:.:-0.00,-1.51,-16.03:46.99:./. |
4987 | 22 | 51224947 | rs6009969 | A | G | . | PASS | DP=3023;AF=0.078;CB=UM,BI,BC;EUR_R2=0.346;AFR_... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:6.17:./. | ... | 0|0:.:.:.:.,.,.:6.17:./. | 0|0:.:.:.:.,.,.:6.17:./. | 0|0:2,2:1:.:-0.00,-0.30,-3.16:8.88:./. | 0|0:.:.:.:.,.,.:6.17:./. | 0|0:.:.:.:.,.,.:6.17:./. | 0|0:5,0:1:.:-0.00,-0.30,-4.07:8.88:./. | 0|0:4,0:2:.:-0.00,-0.60,-7.33:11.59:./. | 0|0:5,0:2:.:-0.00,-0.60,-7.11:11.59:./. | 0|0:10,0:5:.:-0.00,-1.51,-19.50:20.41:./. | 0|0:.:.:.:.,.,.:6.17:./. |
4988 | 22 | 51224993 | rs2595141 | G | C | . | PASS | DP=2322;AF=0.020;CB=BI,BC;EUR_R2=0.59;AFR_R2=0... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:20.55:./. | ... | 0|0:.:.:.:.,.,.:20.55:./. | 0|0:6,1:4:.:-0.00,-1.21,-16.22:32.60:./. | 0|0:2,1:2:.:-0.00,-0.60,-8.84:26.54:./. | 0|0:5,0:3:.:-0.00,-0.90,-13.43:29.51:./. | 0|0:4,0:3:.:-0.00,-0.90,-13.43:29.51:./. | 0|0:6,0:6:.:-0.00,-1.81,-24.96:38.54:./. | 0|0:3,0:3:.:-0.00,-0.90,-12.78:29.51:./. | 0|0:.:.:.:.,.,.:20.55:./. | 0|0:10,0:8:.:-0.00,-2.41,-35.26:45.23:./. | 0|0:2,2:1:.:-0.00,-0.30,-3.85:23.54:./. |
4989 | 22 | 51227891 | rs6010091 | G | A | . | PASS | DP=1953;AF=0.264;CB=UM,BI,BC;EUR_R2=0.429;AFR_... | GT:AD:DP:GD:GL:GQ:OG | 0|0:1,0:1:.:-0.00,-0.30,-2.90:6.41:./. | ... | 0|0:.:.:.:.,.,.:2.29:./. | 0|0:4,0:2:.:-0.00,-0.60,-5.54:12.11:./. | 0|0:.:.:.:.,.,.:1.97:./. | 0|0:.:.:.:.,.,.:4.76:./. | 1|0:0,1:1:.:-3.66,-0.30,-0.00:9.76:1/1 | 1|1:0,6:1:.:-3.66,-0.30,-0.00:2.23:./. | 1|0:0,3:2:.:-7.61,-0.60,-0.00:5.61:1/1 | 0|0:2,0:1:.:-0.00,-0.30,-3.30:8.43:./. | 0|0:6,3:6:.:-0.01,-1.81,-18.29:18.11:./. | 0|0:4,0:2:.:-0.00,-0.60,-6.46:11.17:./. |
4990 | 22 | 51227937 | rs6009970 | A | C | . | PASS | DP=1066;AF=0.997;CB=UM,BI;EUR_R2=0.21;AFR_R2=0... | GT:AD:DP:GD:GL:GQ:OG | 1|1:.:.:.:.,.,.:12.86:./. | ... | 1|1:.:.:.:.,.,.:12.22:./. | 1|1:.:.:.:.,.,.:12.97:./. | 1|1:.:.:.:.,.,.:13.98:./. | 1|1:.:.:.:.,.,.:11.92:./. | 1|1:.:.:.:.,.,.:7.93:./. | 1|1:.:.:.:.,.,.:12.42:./. | 1|1:.:.:.:.,.,.:7.31:./. | 1|1:.:.:.:.,.,.:12.38:./. | 1|1:.:.:.:.,.,.:13.35:./. | 1|1:.:.:.:.,.,.:13.02:./. |
4991 | 22 | 51229805 | rs9616985 | T | C | . | PASS | DP=3300;AF=0.085;CB=UM,BI,BC;EUR_R2=0.724;AFR_... | GT:AD:DP:GD:GL:GQ:OG | 0|0:1,0:1:.:-0.00,-0.30,-4.17:10.71:./. | ... | 0|0:6,1:5:.:-0.00,-1.51,-18.51:23.10:./. | 0|0:12,1:12:.:-0.01,-3.62,-42.46:45.23:./. | 0|1:6,4:6:.:-9.86,-1.81,-11.68:60:./. | 0|0:10,0:5:.:-0.00,-1.51,-18.61:23.21:./. | 0|0:10,0:8:.:-0.01,-2.41,-28.27:32.01:./. | 0|0:9,0:8:.:-0.01,-2.41,-28.88:31.94:./. | 0|0:14,0:12:.:-0.01,-3.62,-44.52:45.23:./. | 0|0:6,0:5:.:-0.00,-1.51,-18.92:23.31:./. | 0|0:8,0:6:.:-0.00,-1.81,-23.46:26.11:./. | 0|0:10,0:7:.:-0.00,-2.11,-26.83:29.28:./. |
4992 | 22 | 51233312 | rs62240043 | A | G | . | PASS | DP=2252;AF=0.078;CB=UM,BI;EUR_R2=0.321;AFR_R2=... | GT:AD:DP:GD:GL:GQ:OG | 0|0:2,0:2:.:-0.00,-0.60,-7.61:13.84:./. | ... | 1|1:0,2:1:.:-3.17,-0.30,-0.00:3.28:./. | 0|0:2,0:1:.:-0.00,-0.30,-3.36:11.02:./. | 0|1:6,2:1:.:-0.00,-0.30,-3.17:2.96:0/0 | 0|0:1,0:1:.:-0.00,-0.30,-3.07:11.02:./. | 0|1:3,4:1:.:-0.00,-0.30,-3.66:2.84:0/0 | 0|1:2,4:1:.:-2.77,-0.30,-0.00:10.71:1/1 | 0|0:.:.:.:.,.,.:8.23:./. | 0|0:6,0:3:.:-0.00,-0.91,-10.07:16.85:./. | 0|0:8,1:1:.:-0.00,-0.30,-3.76:12.02:./. | 0|0:5,0:1:.:-0.00,-0.30,-3.86:12.68:./. |
4993 | 22 | 51233347 | rs62240044 | T | C | . | PASS | DP=2566;AF=0.010;CB=UM,BI;EUR_R2=0.072;AFR_R2=... | GT:AD:DP:GD:GL:GQ:OG | 0|0:2,0:2:.:-0.00,-0.60,-8.23:10.09:./. | ... | 0|0:.:.:.:.,.,.:4.91:./. | 0|0:.:.:.:.,.,.:4.91:./. | 0|0:.:.:.:.,.,.:4.91:./. | 0|0:.:.:.:.,.,.:4.91:./. | 0|0:.:.:.:.,.,.:4.91:./. | 1|0:5,3:1:.:-3.10,-0.30,-0.00:7.46:1/1 | 0|0:.:.:.:.,.,.:4.91:./. | 0|0:.:.:.:.,.,.:4.91:./. | 0|0:.:.:.:.,.,.:4.91:./. | 0|0:.:.:.:.,.,.:4.91:./. |
4994 | 22 | 51234159 | rs8138356 | T | A | . | PASS | DP=2851;AF=0.021;CB=UM,BI;EUR_R2=0.548;AFR_R2=... | GT:AD:DP:GD:GL:GQ:OG | 0|0:2,0:2:.:-0.00,-0.60,-7.64:27.72:./. | ... | 0|0:5,0:2:.:-0.00,-0.60,-7.70:27.72:./. | 0|0:5,0:1:.:-0.00,-0.30,-3.40:24.74:./. | 0|0:10,0:5:.:-0.00,-1.51,-17.03:36.78:./. | 0|0:10,0:4:.:-0.00,-1.21,-13.99:33.77:./. | 0|0:10,0:7:.:-0.01,-2.11,-23.25:43.01:./. | 0|0:7,0:1:.:-0.00,-0.30,-3.60:24.74:./. | 0|0:5,0:1:.:-0.00,-0.30,-3.40:24.74:./. | 0|0:7,0:3:.:-0.00,-0.90,-9.84:30.71:./. | 0|0:4,0:3:.:-0.00,-0.90,-10.24:30.71:./. | 0|0:5,0:1:.:-0.00,-0.30,-3.44:24.74:./. |
4995 | 22 | 51234199 | rs6010092 | T | C | . | PASS | DP=2463;AF=0.006;CB=UM,BI;EUR_R2=0.648;AFR_R2=... | GT:AD:DP:GD:GL:GQ:OG | 0|0:1,0:1:.:-0.00,-0.30,-3.96:25.48:./. | ... | 0|0:1,0:1:.:-0.00,-0.30,-3.97:25.48:./. | 0|0:6,0:6:.:-0.00,-1.81,-21.60:40.46:./. | 0|0:11,0:11:.:-0.01,-3.32,-41.93:60:./. | 0|0:2,0:2:.:-0.00,-0.60,-7.62:28.48:./. | 0|0:11,0:9:.:-0.01,-2.72,-32.46:50:./. | 0|0:11,0:10:.:-0.00,-3.01,-36.92:50:./. | 0|0:6,0:5:.:-0.01,-1.51,-17.11:37.45:./. | 0|0:8,0:7:.:-0.00,-2.11,-25.95:43.98:./. | 0|0:10,0:10:.:-0.00,-3.01,-38.82:50:./. | 0|0:8,0:8:.:-0.00,-2.41,-29.28:46.99:./. |
4996 | 22 | 51234632 | rs6010093 | G | C | . | PASS | DP=2243;AF=0.003;CB=UM,BI;AFR_R2=0.658 | GT:AD:DP:GD:GL:GQ:OG | ./.:.:.:.:.,.,.:.:./. | ... | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. | ./.:.:.:.:.,.,.:.:./. |
4997 | 22 | 51235344 | rs114148499 | G | A | . | PASS | DP=2322;AF=0.030;CB=UM,BI,BC;EUR_R2=0.548;AFR_... | GT:AD:DP:GD:GL:GQ:OG | 0|0:2,0:2:.:-0.00,-0.60,-7.26:14.83:./. | ... | 0|0:2,0:2:.:-0.00,-0.60,-7.19:14.62:./. | 0|0:4,0:3:.:-0.00,-0.91,-8.43:17.62:./. | 0|0:4,0:3:.:-0.00,-0.90,-9.11:17.63:./. | 0|0:3,0:1:.:-0.00,-0.30,-3.50:11.85:./. | 0|0:3,0:3:.:-0.00,-0.90,-9.03:17.60:./. | 0|0:6,0:3:.:-0.00,-0.90,-9.63:17.62:./. | 0|0:2,0:2:.:-0.00,-0.60,-7.49:14.71:./. | 0|0:.:.:.:.,.,.:9:./. | 0|0:.:.:.:.,.,.:9.08:./. | 0|0:.:.:.:.,.,.:8.86:./. |
4998 | 22 | 51237063 | rs3896457 | T | C | . | PASS | DP=2410;AF=0.136;CB=UM,BI;EUR_R2=0.25;AFR_R2=0.46 | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:3.27:./. | ... | 0|0:.:.:.:.,.,.:3.06:./. | 0|0:.:.:.:.,.,.:3.06:./. | 0|0:.:.:.:.,.,.:3.06:./. | 0|1:2,1:1:.:-3.37,-0.30,-0.00:5.39:1/1 | 0|0:.:.:.:.,.,.:3.06:./. | 0|0:.:.:.:.,.,.:3.06:./. | 1|1:1,2:2:.:-5.96,-0.60,-0.00:2.80:./. | 0|0:.:.:.:.,.,.:3.06:./. | 0|1:4,2:1:.:-3.27,-0.30,-0.00:5.39:1/1 | 0|0:.:.:.:.,.,.:3.06:./. |
4999 | 22 | 51238831 | rs62240048 | C | T | . | PASS | DP=2392;AF=0.268;CB=UM,BI;EUR_R2=0.392;AFR_R2=... | GT:AD:DP:GD:GL:GQ:OG | 0|0:.:.:.:.,.,.:8.45:./. | ... | 0|0:4,2:4:.:-0.00,-1.21,-12.40:20.10:./. | 0|0:.:.:.:.,.,.:8.45:./. | 0|0:3,4:2:.:-0.00,-0.60,-6.14:14.13:./. | 0|1:0,2:1:.:-3.97,-0.30,-0.00:11.31:1/1 | 0|0:6,2:4:.:-0.01,-1.21,-11.53:20:./. | 0|0:8,1:6:.:-0.01,-1.81,-18.14:25.97:./. | 0|0:1,3:1:.:-0.00,-0.30,-2.77:11.29:./. | 0|0:2,2:1:.:-0.00,-0.30,-2.97:11.29:./. | 0|0:7,0:5:.:-0.01,-1.51,-14.73:22.97:./. | 0|0:5,0:3:.:-0.00,-0.91,-8.93:17.14:./. |
5000 rows × 638 columns
sample_ids = list(df.columns[9:])
len(sample_ids)
629
sample_ids_number = ['{} num'.format(s) for s in sample_ids]
def get_number(ref, alt):
if ',' in alt or '.' in ref or '.' in alt:
return np.nan
return sum(map(int, [ref, alt]))
def call_genotype_number(row):
return pd.Series(
[get_number(row[s][0], row[s][2]) for s in sample_ids if s],
index=sample_ids_number)
df[sample_ids_number] = df.apply(call_genotype_number, axis=1)
matrix = df[sample_ids_number].T
matrix
0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | ... | 4990 | 4991 | 4992 | 4993 | 4994 | 4995 | 4996 | 4997 | 4998 | 4999 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
HG00098 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00100 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00106 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 |
HG00112 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00114 num | NaN | NaN | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 |
HG00116 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 2.0 | 0.0 |
HG00117 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00118 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00119 num | NaN | NaN | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 |
HG00120 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 |
HG00122 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00123 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00124 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00126 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00131 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 |
HG00141 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00142 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 1.0 |
HG00143 num | NaN | NaN | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00144 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00145 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00146 num | NaN | NaN | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 2.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 |
HG00147 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00148 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 |
HG00149 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 1.0 |
HG00150 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 1.0 |
HG00151 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
HG00152 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | NaN | 1.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 |
HG00153 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 |
HG00156 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 |
HG00158 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
NA20786 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 |
NA20787 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20790 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20792 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20795 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 2.0 | 1.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 |
NA20796 num | NaN | NaN | 0.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20797 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20798 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | NaN | 1.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 0.0 | 0.0 |
NA20799 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20800 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 0.0 | 0.0 |
NA20801 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20802 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20803 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 1.0 | 0.0 |
NA20804 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20805 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20806 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | NaN | 1.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 |
NA20807 num | NaN | NaN | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 2.0 | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 |
NA20808 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20809 num | NaN | NaN | 1.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 2.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 0.0 | 0.0 |
NA20810 num | NaN | NaN | 2.0 | 2.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 2.0 | ... | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 0.0 | 0.0 |
NA20811 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20812 num | NaN | NaN | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20813 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20814 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 |
NA20815 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20816 num | NaN | NaN | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 2.0 | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20818 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 2.0 | 0.0 |
NA20819 num | NaN | NaN | 1.0 | 2.0 | 1.0 | 0.0 | 0.0 | 1.0 | NaN | 2.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
NA20826 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 |
NA20828 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 |
629 rows × 5000 columns
sample_df = pd.read_excel('1KG_sample_info.xlsx')
sample_df
Sample | Family ID | Population | Population Description | Gender | Relationship | Unexpected Parent/Child | Non Paternity | Siblings | Grandparents | Avuncular | Half Siblings | Unknown Second Order | Third Order | Other Comments | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | HG00096 | HG00096 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
1 | HG00097 | HG00097 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
2 | HG00098 | HG00098 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3 | HG00099 | HG00099 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
4 | HG00100 | HG00100 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
5 | HG00101 | HG00101 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
6 | HG00102 | HG00102 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
7 | HG00103 | HG00103 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
8 | HG00104 | HG00104 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
9 | HG00105 | HG00105 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
10 | HG00106 | HG00106 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
11 | HG00107 | HG00107 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
12 | HG00108 | HG00108 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
13 | HG00109 | HG00109 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
14 | HG00110 | HG00110 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
15 | HG00111 | HG00111 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
16 | HG00112 | HG00112 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
17 | HG00113 | HG00113 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
18 | HG00114 | HG00114 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
19 | HG00115 | HG00115 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
20 | HG00116 | HG00116 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
21 | HG00117 | HG00117 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
22 | HG00118 | HG00118 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
23 | HG00119 | HG00119 | GBR | British in England and Scotland | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | HG00124 | NaN | NaN |
24 | HG00120 | HG00120 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
25 | HG00121 | HG00121 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
26 | HG00122 | HG00122 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
27 | HG00123 | HG00123 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
28 | HG00124 | HG00124 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | HG00119 | NaN | NaN |
29 | HG00125 | HG00125 | GBR | British in England and Scotland | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
3470 | NA21109 | NA21109 | GIH | Gujarati Indian in Houston,TX | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3471 | NA21110 | NA21110 | GIH | Gujarati Indian in Houston,TX | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3472 | NA21111 | NA21111 | GIH | Gujarati Indian in Houston,TX | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3473 | NA21112 | NA21112 | GIH | Gujarati Indian in Houston,TX | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3474 | NA21113 | NA21113 | GIH | Gujarati Indian in Houston,TX | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3475 | NA21114 | NA21114 | GIH | Gujarati Indian in Houston,TX | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NA21134 | NaN |
3476 | NA21115 | NA21115 | GIH | Gujarati Indian in Houston,TX | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3477 | NA21116 | NA21116 | GIH | Gujarati Indian in Houston,TX | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3478 | NA21117 | NA21117 | GIH | Gujarati Indian in Houston,TX | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3479 | NA21118 | NA21118 | GIH | Gujarati Indian in Houston,TX | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3480 | NA21119 | NA21119 | GIH | Gujarati Indian in Houston,TX | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3481 | NA21120 | NA21120 | GIH | Gujarati Indian in Houston,TX | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3482 | NA21121 | NA21121 | GIH | Gujarati Indian in Houston,TX | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3483 | NA21122 | NA21122 | GIH | Gujarati Indian in Houston,TX | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3484 | NA21123 | NA21123 | GIH | Gujarati Indian in Houston,TX | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3485 | NA21124 | NA21124 | GIH | Gujarati Indian in Houston,TX | male | unrel | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3486 | NA21125 | NA21125 | GIH | Gujarati Indian in Houston,TX | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3487 | NA21126 | NA21126 | GIH | Gujarati Indian in Houston,TX | male | unrel | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3488 | NA21127 | NA21127 | GIH | Gujarati Indian in Houston,TX | male | unrel | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3489 | NA21128 | NA21128 | GIH | Gujarati Indian in Houston,TX | male | unrel | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3490 | NA21129 | NA21129 | GIH | Gujarati Indian in Houston,TX | male | unrel | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3491 | NA21130 | NA21130 | GIH | Gujarati Indian in Houston,TX | male | unrel | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3492 | NA21133 | NA21133 | GIH | Gujarati Indian in Houston,TX | male | unrel | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3493 | NA21134 | NA21134 | GIH | Gujarati Indian in Houston,TX | male | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NA21114 | NaN |
3494 | NA21135 | NA21135 | GIH | Gujarati Indian in Houston,TX | male | unrel | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3495 | NA21137 | NA21137 | GIH | Gujarati Indian in Houston,TX | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3496 | NA21141 | NA21141 | GIH | Gujarati Indian in Houston,TX | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3497 | NA21142 | NA21142 | GIH | Gujarati Indian in Houston,TX | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3498 | NA21143 | NA21143 | GIH | Gujarati Indian in Houston,TX | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3499 | NA21144 | NA21144 | GIH | Gujarati Indian in Houston,TX | female | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
3500 rows × 15 columns
sample_dict = {}
for i, r in sample_df.iterrows():
sample_dict[r['Sample']] = r['Population']
sample_dict
{'HG03351': 'ESN', 'HG01677': 'IBS', 'HG01789': 'GBR', 'HG03510': 'ESN', 'HG00641': 'PUR', 'HG01596': 'KHV', 'NA11839': 'CEU', 'HG02786': 'PJL', 'HG02733': 'PJL', 'HG02382': 'CDX', 'HG00105': 'GBR', 'HG00664': 'CHS', 'NA20292': 'ASW', 'NA19154': 'YRI', 'HG02406': 'CDX', 'HG03393': 'MSL', 'HG01531': 'IBS', 'NA19788': 'MXL', 'HG03269': 'ESN', 'HG02451': 'ACB', 'HG03778': 'ITU', 'NA12812': 'CEU', 'NA20753': 'TSI', 'HG01675': 'IBS', 'NA20333': 'ASW', 'HG01858': 'KHV', 'HG03863': 'ITU', 'HG04156': 'BEB', 'NA19086': 'JPT', 'NA20533': 'TSI', 'HG01439': 'CLM', 'HG03095': 'MSL', 'HG02721': 'GWD', 'NA20905': 'GIH', 'NA10856': 'CEU', 'NA18582': 'CHB', 'NA20805': 'TSI', 'NA18592': 'CHB', 'NA18544': 'CHB', 'HG00369': 'FIN', 'HG03490': 'PJL', 'NA20512': 'TSI', 'HG00578': 'CHS', 'HG03995': 'STU', 'NA19141': 'YRI', 'HG00584': 'CHS', 'HG02255': 'ACB', 'NA21125': 'GIH', 'NA18951': 'JPT', 'HG03104': 'ESN', 'HG03556': 'MSL', 'HG01891': 'ACB', 'HG03166': 'ESN', 'HG03947': 'STU', 'HG01377': 'CLM', 'HG00372': 'FIN', 'HG01840': 'KHV', 'HG03896': 'STU', 'NA20355': 'ASW', 'HG01710': 'IBS', 'HG02184': 'CDX', 'HG01174': 'PUR', 'HG02568': 'GWD', 'HG02861': 'GWD', 'HG02231': 'IBS', 'HG02256': 'ACB', 'HG02489': 'ACB', 'HG00101': 'GBR', 'NA19307': 'LWK', 'HG02442': 'ACB', 'NA19775': 'MXL', 'NA21091': 'GIH', 'NA19784': 'MXL', 'HG01777': 'IBS', 'HG01273': 'CLM', 'HG03066': 'MSL', 'HG03788': 'ITU', 'HG01870': 'KHV', 'NA19836': 'ASW', 'NA19789': 'MXL', 'NA20530': 'TSI', 'HG03452': 'MSL', 'HG01167': 'PUR', 'HG03058': 'MSL', 'NA12864': 'CEU', 'HG03701': 'PJL', 'HG00139': 'GBR', 'HG02106': 'PEL', 'HG02004': 'PEL', 'NA20357': 'ASW', 'HG01928': 'PEL', 'NA20876': 'GIH', 'HG02490': 'PJL', 'HG00447': 'CHS', 'HG02455': 'ACB', 'HG01950': 'PEL', 'HG01379': 'CLM', 'HG03928': 'BEB', 'NA10850': 'CEU', 'HG04202': 'ITU', 'NA21144': 'GIH', 'HG02879': 'GWD', 'NA20816': 'TSI', 'HG03857': 'STU', 'HG00685': 'CHS', 'HG02612': 'GWD', 'HG02102': 'PEL', 'NA12056': 'CEU', 'HG02924': 'ESN', 'HG00594': 'CHS', 'HG03901': 'BEB', 'HG01369': 'CLM', 'HG03164': 'ESN', 'NA20276': 'ASW', 'NA19384': 'LWK', 'NA20787': 'TSI', 'NA19762': 'MXL', 'NA18623': 'CHB', 'HG03742': 'ITU', 'HG01031': 'CDX', 'HG01280': 'CLM', 'HG01347': 'CLM', 'HG03762': 'PJL', 'NA18933': 'YRI', 'NA12828': 'CEU', 'NA18935': 'YRI', 'HG02577': 'ACB', 'HG03906': 'BEB', 'HG01394': 'PUR', 'NA19024': 'LWK', 'NA19019': 'LWK', 'HG03091': 'MSL', 'HG01028': 'CDX', 'NA19678': 'MXL', 'NA19771': 'MXL', 'HG03972': 'ITU', 'HG00157': 'GBR', 'HG00156': 'GBR', 'HG03593': 'BEB', 'NA19440': 'LWK', 'HG04115': 'STU', 'NA19680': 'MXL', 'HG01334': 'GBR', 'HG00614': 'CHS', 'HG04302': 'GBR', 'HG02775': 'PJL', 'NA20364': 'ASW', 'NA19377': 'LWK', 'NA19787': 'MXL', 'NA21105': 'GIH', 'HG01105': 'PUR', 'HG03137': 'ESN', 'HG02501': 'ACB', 'HG03657': 'PJL', 'HG01590': 'PJL', 'HG03679': 'STU', 'HG00308': 'FIN', 'HG00600': 'CHS', 'HG00844': 'CDX', 'NA19056': 'JPT', 'NA06986': 'CEU', 'NA19900': 'ASW', 'HG03115': 'ESN', 'NA19077': 'JPT', 'NA19444': 'LWK', 'HG01081': 'PUR', 'HG02030': 'KHV', 'HG02397': 'CDX', 'NA20581': 'TSI', 'HG02132': 'KHV', 'HG02012': 'ACB', 'HG03228': 'PJL', 'NA12892': 'CEU', 'HG02020': 'KHV', 'HG00444': 'CHS', 'HG03940': 'BEB', 'HG04118': 'ITU', 'NA20891': 'GIH', 'HG03840': 'STU', 'HG03683': 'STU', 'HG01790': 'GBR', 'HG01308': 'PUR', 'HG00310': 'FIN', 'NA19097': 'YRI', 'HG03693': 'STU', 'HG01134': 'CLM', 'HG00622': 'CHS', 'HG02477': 'ACB', 'HG02085': 'KHV', 'NA12740': 'CEU', 'HG03026': 'GWD', 'HG03752': 'STU', 'HG01630': 'IBS', 'NA20881': 'GIH', 'NA18534': 'CHB', 'NA20882': 'GIH', 'NA07349': 'CEU', 'HG03583': 'MSL', 'NA07014': 'CEU', 'HG03806': 'BEB', 'HG01926': 'PEL', 'HG01890': 'ACB', 'NA19085': 'JPT', 'HG03419': 'MSL', 'HG01029': 'CDX', 'NA19428': 'LWK', 'HG02077': 'KHV', 'NA10864': 'CEU', 'HG03445': 'MSL', 'HG03754': 'STU', 'HG03381': 'MSL', 'HG02387': 'CDX', 'HG01981': 'PEL', 'HG01176': 'PUR', 'NA20291': 'ASW', 'HG01150': 'CLM', 'HG01050': 'PUR', 'NA19030': 'LWK', 'HG01783': 'IBS', 'HG03160': 'ESN', 'HG02810': 'GWD', 'HG00407': 'CHS', 'HG01605': 'IBS', 'HG02685': 'PJL', 'HG00306': 'FIN', 'NA19140': 'YRI', 'HG04080': 'ITU', 'NA12717': 'CEU', 'NA18626': 'CHB', 'HG01254': 'CLM', 'HG02139': 'KHV', 'HG03604': 'BEB', 'HG03660': 'PJL', 'HG02358': 'CDX', 'NA19084': 'JPT', 'NA18505': 'YRI', 'HG00867': 'CDX', 'NA20520': 'TSI', 'HG03982': 'STU', 'HG03874': 'ITU', 'HG02013': 'ACB', 'HG00187': 'FIN', 'HG00250': 'GBR', 'NA19116': 'YRI', 'HG02505': 'ACB', 'NA20312': 'ASW', 'HG03167': 'ESN', 'NA19792': 'MXL', 'NA21142': 'GIH', 'HG00124': 'GBR', 'NA21143': 'GIH', 'HG02716': 'GWD', 'HG00864': 'CDX', 'HG00100': 'GBR', 'HG02526': 'KHV', 'NA19160': 'YRI', 'NA19662': 'MXL', 'HG02464': 'GWD', 'NA19122': 'YRI', 'HG02722': 'GWD', 'HG00376': 'FIN', 'HG03832': 'BEB', 'HG03473': 'MSL', 'HG01258': 'CLM', 'NA20871': 'GIH', 'HG03733': 'STU', 'HG04003': 'STU', 'NA18794': 'CHB', 'HG03339': 'ESN', 'HG02597': 'PJL', 'HG01702': 'IBS', 'HG00599': 'CHS', 'HG03944': 'STU', 'NA20845': 'GIH', 'HG00596': 'CHS', 'HG02891': 'GWD', 'HG00110': 'GBR', 'HG01454': 'CLM', 'HG00730': 'CHS', 'HG02811': 'GWD', 'NA20785': 'TSI', 'HG00632': 'CHS', 'NA20504': 'TSI', 'HG03571': 'MSL', 'HG00135': 'GBR', 'NA20875': 'GIH', 'HG00245': 'GBR', 'HG01667': 'IBS', 'HG04171': 'BEB', 'HG02318': 'ACB', 'NA20346': 'ASW', 'HG00428': 'CHS', 'HG03721': 'ITU', 'HG02570': 'GWD', 'NA20518': 'TSI', 'NA19079': 'JPT', 'HG00672': 'CHS', 'NA12282': 'CEU', 'HG02323': 'ACB', 'NA19682': 'MXL', 'HG03056': 'MSL', 'HG03361': 'ESN', 'NA21088': 'GIH', 'HG02584': 'GWD', 'NA18967': 'JPT', 'NA19463': 'LWK', 'HG02768': 'GWD', 'HG03654': 'PJL', 'HG03129': 'ESN', 'NA18498': 'YRI', 'NA20525': 'TSI', 'HG02040': 'KHV', 'HG02058': 'KHV', 'NA20587': 'TSI', 'HG04206': 'ITU', 'HG03629': 'PJL', 'HG01532': 'IBS', 'HG03451': 'MSL', 'NA06994': 'CEU', 'HG02623': 'GWD', 'NA20870': 'GIH', 'HG02880': 'GWD', 'NA18628': 'CHB', 'HG04056': 'ITU', 'NA18867': 'YRI', 'HG00103': 'GBR', 'HG02152': 'CDX', 'HG04070': 'ITU', 'HG02799': 'GWD', 'HG01149': 'CLM', 'HG03508': 'ESN', 'HG02660': 'PJL', 'NA19776': 'MXL', 'HG03055': 'MSL', 'HG01998': 'PEL', 'HG01247': 'PUR', 'NA20821': 'TSI', 'HG03804': 'BEB', 'HG01279': 'CLM', 'HG03465': 'MSL', 'HG03474': 'MSL', 'HG03868': 'ITU', 'NA19324': 'LWK', 'HG02156': 'CDX', 'NA18941': 'JPT', 'HG03248': 'GWD', 'HG01433': 'CLM', 'NA10840': 'CEU', 'NA20541': 'TSI', 'HG03116': 'ESN', 'HG01686': 'IBS', 'HG02046': 'KHV', 'HG03303': 'ESN', 'HG03741': 'STU', 'HG03297': 'ESN', 'HG02367': 'CDX', 'HG03799': 'BEB', 'HG01357': 'CLM', 'NA18630': 'CHB', 'HG04208': 'STU', 'NA21086': 'GIH', 'HG03082': 'MSL', 'HG02462': 'GWD', 'HG01073': 'PUR', 'NA19652': 'MXL', 'HG03985': 'STU', 'HG01775': 'IBS', 'HG03691': 'STU', 'NA18577': 'CHB', 'NA18881': 'YRI', 'NA20831': 'TSI', 'NA19394': 'LWK', 'HG01880': 'ACB', 'HG02304': 'PEL', 'NA20300': 'ASW', 'HG02379': 'CDX', 'NA20511': 'TSI', 'HG00592': 'CHS', 'HG00188': 'FIN', 'NA19063': 'JPT', 'HG03729': 'ITU', 'NA19132': 'YRI', 'NA18966': 'JPT', 'NA20810': 'TSI', 'HG02312': 'PEL', 'HG01965': 'PEL', 'NA19159': 'YRI', 'NA12815': 'CEU', 'HG01997': 'PEL', 'HG01187': 'PUR', 'NA12154': 'CEU', 'HG02537': 'ACB', 'HG03908': 'BEB', 'NA19834': 'ASW', 'HG01942': 'PEL', 'HG03669': 'PJL', 'NA19683': 'MXL', 'HG02006': 'PEL', 'HG02661': 'PJL', 'NA19055': 'JPT', 'HG01361': 'CLM', 'HG03126': 'ESN', 'HG03802': 'BEB', 'HG01489': 'CLM', 'NA18615': 'CHB', 'NA18944': 'JPT', 'HG00189': 'FIN', 'HG00633': 'CHS', 'HG01106': 'PUR', 'NA20754': 'TSI', 'NA19161': 'YRI', 'HG02725': 'PJL', 'HG00351': 'FIN', 'NA20815': 'TSI', 'NA12058': 'CEU', 'HG02150': 'PEL', 'HG00249': 'GBR', 'HG00465': 'CHS', 'HG00453': 'CHS', 'HG00178': 'FIN', 'HG02075': 'KHV', 'HG02347': 'PEL', 'HG03814': 'BEB', 'NA12336': 'CEU', 'HG00690': 'CHS', 'HG02890': 'GWD', 'HG03743': 'STU', 'NA18485': 'YRI', 'HG01968': 'PEL', 'HG01441': 'CLM', 'HG00625': 'CHS', 'HG03793': 'BEB', 'HG02471': 'ACB', 'NA07029': 'CEU', 'HG00619': 'CHS', 'HG04164': 'BEB', 'NA18617': 'CHB', 'HG02947': 'ESN', 'HG03128': 'ESN', 'NA20296': 'ASW', 'HG02821': 'GWD', 'NA18536': 'CHB', 'HG00129': 'GBR', 'HG00321': 'FIN', 'HG03522': 'ESN', 'NA19316': 'LWK', 'HG03808': 'BEB', 'HG01774': 'IBS', 'HG03926': 'BEB', 'HG03376': 'MSL', 'NA19461': 'LWK', 'NA20585': 'TSI', 'HG00141': 'GBR', 'NA19127': 'YRI', 'HG02466': 'GWD', 'HG01367': 'CLM', 'HG02272': 'PEL', 'HG02317': 'ACB', 'HG03492': 'PJL', 'NA20519': 'TSI', 'HG01954': 'PEL', 'HG03700': 'PJL', 'HG01868': 'KHV', 'NA19012': 'JPT', 'NA19149': 'YRI', 'NA19190': 'YRI', 'HG01048': 'PUR', 'HG02385': 'CDX', 'HG03858': 'STU', 'NA20786': 'TSI', 'NA19448': 'LWK', 'NA18917': 'YRI', 'HG04194': 'BEB', 'NA19002': 'JPT', 'HG03909': 'BEB', 'HG04191': 'BEB', 'HG00866': 'CDX', 'NA19332': 'LWK', 'HG04036': 'STU', 'HG02166': 'CDX', 'HG02851': 'GWD', 'NA19908': 'ASW', 'HG03027': 'GWD', 'NA20529': 'TSI', 'NA20854': 'GIH', 'HG00472': 'CHS', 'NA18486': 'YRI', 'HG01748': 'IBS', 'HG04141': 'BEB', 'HG02134': 'KHV', 'NA12877': 'CEU', 'HG02521': 'KHV', 'HG03062': 'MSL', 'HG02737': 'PJL', 'HG03969': 'ITU', 'HG01346': 'CLM', 'HG01883': 'ACB', 'HG02495': 'PJL', 'HG02727': 'PJL', 'HG04015': 'ITU', 'HG01769': 'IBS', 'HG01305': 'PUR', 'HG00530': 'CHS', 'HG00280': 'FIN', 'NA18538': 'CHB', 'HG01453': 'CLM', 'HG01261': 'CLM', 'NA07345': 'CEU', 'HG03720': 'ITU', 'HG01845': 'KHV', 'HG03022': 'PJL', 'HG03266': 'ESN', 'HG01248': 'PUR', 'HG02798': 'GWD', 'HG03783': 'ITU', 'NA18948': 'JPT', 'NA21129': 'GIH', 'NA12762': 'CEU', 'HG01626': 'IBS', 'NA19027': 'LWK', 'NA20321': 'ASW', 'NA20869': 'GIH', 'HG03785': 'ITU', 'HG02885': 'GWD', 'HG00113': 'GBR', 'HG00607': 'CHS', 'HG03454': 'MSL', 'HG03824': 'BEB', 'NA20535': 'TSI', 'HG02555': 'ACB', 'NA19731': 'MXL', 'HG02770': 'GWD', 'HG03744': 'STU', 'HG01323': 'PUR', 'HG03702': 'PJL', 'HG04058': 'ITU', 'NA18878': 'YRI', 'NA18497': 'YRI', 'HG03251': 'GWD', 'HG02130': 'KHV', 'HG00313': 'FIN', 'NA18985': 'JPT', 'HG02780': 'PJL', 'HG03617': 'BEB', 'HG00364': 'FIN', 'NA18621': 'CHB', 'HG01849': 'KHV', 'HG01948': 'PEL', 'HG01960': 'ACB', 'NA12275': 'CEU', 'HG02889': 'GWD', 'HG01253': 'CLM', 'HG00699': 'CHS', 'HG01342': 'CLM', 'NA18970': 'JPT', 'NA20302': 'ASW', 'HG00375': 'FIN', 'HG02410': 'CDX', 'HG01914': 'ACB', 'HG03127': 'ESN', 'HG03134': 'ESN', 'HG03517': 'ESN', 'HG02807': 'GWD', 'HG03789': 'ITU', 'NA12767': 'CEU', 'NA10855': 'CEU', 'NA19663': 'MXL', 'HG02808': 'GWD', 'NA18643': 'CHB', 'HG00315': 'FIN', 'HG02217': 'IBS', 'NA20540': 'TSI', 'HG02419': 'ACB', 'HG02127': 'KHV', 'HG00556': 'CHS', 'HG00182': 'FIN', 'HG01551': 'CLM', 'HG00738': 'PUR', 'HG03760': 'STU', 'HG03344': 'ESN', 'HG04002': 'ITU', 'HG02439': 'ACB', 'NA20861': 'GIH', 'HG03124': 'ESN', 'HG03978': 'ITU', 'NA18525': 'CHB', 'HG00422': 'CHS', 'HG02511': 'ACB', 'HG02596': 'GWD', 'HG00362': 'FIN', 'HG01566': 'PEL', 'NA19471': 'LWK', 'HG00450': 'CHS', 'HG00149': 'GBR', 'NA20414': 'ASW', 'HG02595': 'GWD', 'HG02073': 'KHV', 'HG02610': 'GWD', 'NA19430': 'LWK', 'HG00099': 'GBR', 'HG00579': 'CHS', 'HG03844': 'STU', 'HG01536': 'IBS', 'HG00104': 'GBR', 'HG00566': 'CHS', 'HG03385': 'MSL', 'NA19254': 'YRI', 'HG03953': 'STU', 'HG03919': 'BEB', 'HG00533': 'CHS', 'HG02736': 'PJL', 'NA19153': 'YRI', 'HG02089': 'PEL', 'HG03910': 'BEB', 'HG02356': 'CDX', 'NA19984': 'ASW', 'NA20313': 'ASW', 'HG03949': 'STU', 'NA12329': 'CEU', 'NA19214': 'YRI', 'HG01359': 'CLM', 'NA19902': 'ASW', 'NA19671': 'MXL', 'HG03920': 'BEB', 'HG03766': 'PJL', 'HG01241': 'PUR', 'HG02624': 'GWD', 'NA10859': 'CEU', 'NA18960': 'JPT', 'NA18558': 'CHB', 'NA19723': 'MXL', 'HG04076': 'ITU', 'HG00285': 'FIN', 'NA19025': 'LWK', 'HG01063': 'PUR', 'NA19704': 'ASW', 'HG01138': 'CLM', 'NA19755': 'MXL', 'HG00709': 'CHS', 'NA19017': 'LWK', 'HG01122': 'CLM', 'HG03457': 'MSL', 'NA07000': 'CEU', 'HG02800': 'GWD', 'HG02557': 'ACB', 'HG01068': 'PUR', 'HG01850': 'KHV', 'NA12739': 'CEU', 'HG03008': 'BEB', 'HG00611': 'CHS', 'HG02178': 'CDX', 'NA18566': 'CHB', 'HG00623': 'CHS', 'HG02008': 'PEL', 'HG01988': 'ACB', 'NA11832': 'CEU', 'NA20126': 'ASW', 'NA19138': 'YRI', 'NA18565': 'CHB', 'NA18606': 'CHB', 'NA20902': 'GIH', 'HG03021': 'PJL', 'HG01967': 'PEL', 'HG03130': 'ESN', 'NA20828': 'TSI', 'HG01502': 'IBS', 'HG00111': 'GBR', 'HG02698': 'PJL', 'NA19714': 'ASW', 'NA19659': 'MXL', 'HG00638': 'PUR', 'HG01284': 'CLM', 'HG02731': 'PJL', 'HG02757': 'GWD', 'HG01969': 'PEL', 'HG01508': 'IBS', 'HG02971': 'ESN', 'NA19746': 'MXL', 'NA19914': 'ASW', 'NA19338': 'LWK', 'HG03237': 'PJL', 'HG00409': 'CHS', 'HG01985': 'ACB', 'HG01477': 'CLM', 'HG03625': 'PJL', 'HG03870': 'ITU', 'NA19438': 'LWK', 'HG01302': 'PUR', 'HG02285': 'PEL', 'HG01108': 'PUR', 'HG00978': 'CDX', 'HG01274': 'CLM', 'HG02613': 'GWD', 'HG03225': 'MSL', 'HG03135': 'ESN', 'NA19319': 'LWK', 'NA12753': 'CEU', 'HG00589': 'CHS', 'HG02964': 'ESN', 'NA20829': 'TSI', 'NA21111': 'GIH', 'HG02250': 'CDX', 'HG02337': 'ACB', 'NA11917': 'CEU', 'NA19390': 'LWK', 'HG00357': 'FIN', 'HG02237': 'IBS', 'HG03194': 'ESN', 'NA19648': 'MXL', 'HG01761': 'IBS', 'HG03831': 'BEB', 'HG01757': 'IBS', 'HG00628': 'CHS', 'HG00634': 'CHS', 'NA11840': 'CEU', 'HG03247': 'GWD', 'HG03539': 'GWD', 'HG04181': 'BEB', 'NA18911': 'YRI', 'HG01936': 'PEL', 'NA19328': 'LWK', 'HG02652': 'PJL', 'NA18591': 'CHB', 'HG00463': 'CHS', 'HG01669': 'IBS', 'HG01943': 'PEL', 'HG03578': 'MSL', 'HG02724': 'PJL', 'HG03455': 'MSL', 'NA18860': 'YRI', 'HG03391': 'MSL', 'NA19173': 'YRI', 'HG02146': 'PEL', 'HG00356': 'FIN', 'HG00142': 'GBR', 'HG03767': 'PJL', 'HG02267': 'PEL', 'HG03063': 'MSL', 'NA06991': 'CEU', 'NA12865': 'CEU', 'NA19247': 'YRI', 'NA20802': 'TSI', 'HG01620': 'IBS', 'HG03293': 'ESN', 'HG01183': 'PUR', 'NA20299': 'ASW', 'HG03446': 'MSL', 'HG00277': 'FIN', 'HG01175': 'PUR', 'HG00320': 'FIN', 'HG03717': 'ITU', 'NA18564': 'CHB', 'HG01627': 'IBS', 'HG03488': 'PJL', 'HG01951': 'PEL', 'HG00154': 'GBR', 'HG02330': 'ACB', 'HG02965': 'ESN', 'HG03486': 'MSL', 'NA19090': 'JPT', 'HG03963': 'ITU', 'NA19238': 'YRI', 'HG00983': 'CDX', 'HG02980': 'ESN', 'HG01136': 'CLM', 'HG02982': 'GWD', 'NA19093': 'YRI', 'HG02476': 'ACB', 'NA12249': 'CEU', 'HG01706': 'IBS', 'NA19778': 'MXL', 'NA20910': 'GIH', 'NA12043': 'CEU', 'NA18542': 'CHB', 'HG00328': 'FIN', 'NA18934': 'YRI', 'NA18923': 'YRI', 'NA12750': 'CEU', 'HG00116': 'GBR', 'HG03879': 'ITU', 'HG02148': 'PEL', 'NA12044': 'CEU', 'NA19764': 'MXL', 'HG03354': 'ESN', 'HG01126': 'CLM', 'HG04114': 'STU', 'HG01934': 'PEL', 'HG00502': 'CHS', 'HG01841': 'KHV', 'HG00403': 'CHS', 'HG00532': 'CHS', 'NA18979': 'JPT', 'HG01052': 'PUR', 'NA19828': 'ASW', 'HG02380': 'CDX', 'HG03732': 'ITU', 'HG02547': 'ACB', 'NA20863': 'GIH', 'HG03547': 'MSL', 'NA19347': 'LWK', 'HG03052': 'MSL', 'HG03703': 'PJL', 'NA20314': 'ASW', 'NA21118': 'GIH', 'HG04228': 'STU', 'HG02108': 'ACB', 'NA11891': 'CEU', 'NA19749': 'MXL', 'NA18521': 'YRI', 'NA19685': 'MXL', 'NA19171': 'YRI', 'HG00126': 'GBR', 'NA20277': 'ASW', 'HG02233': 'IBS', 'NA18865': 'YRI', 'NA19664': 'MXL', 'HG03017': 'PJL', 'HG00353': 'FIN', 'NA10854': 'CEU', 'NA18504': 'YRI', 'HG03816': 'BEB', 'NA21087': 'GIH', 'NA21099': 'GIH', 'HG01984': 'PEL', 'HG03121': 'ESN', 'NA18632': 'CHB', 'HG03240': 'GWD', 'HG00476': 'CHS', 'HG02360': 'CDX', 'HG03491': 'PJL', 'HG01946': 'PEL', 'HG01987': 'ACB', 'HG03639': 'PJL', 'NA19360': 'LWK', 'HG00381': 'FIN', 'NA20798': 'TSI', 'HG01556': 'CLM', 'HG02377': 'CDX', 'HG02131': 'KHV', 'NA18852': 'YRI', 'HG03513': 'ESN', 'HG04217': 'ITU', 'HG03054': 'MSL', 'NA19235': 'YRI', 'HG01684': 'IBS', 'HG02262': 'PEL', 'HG00612': 'CHS', 'NA21137': 'GIH', 'NA18978': 'JPT', 'NA20362': 'ASW', 'HG02224': 'IBS', 'HG03161': 'ESN', 'HG01978': 'PEL', 'HG04024': 'ITU', 'HG00627': 'CHS', 'HG03079': 'MSL', 'NA19730': 'MXL', 'HG02883': 'GWD', 'HG02541': 'ACB', 'HG00543': 'CHS', 'NA19248': 'YRI', 'NA18795': 'CHB', 'HG01679': 'IBS', 'HG02259': 'PEL', 'NA20297': 'ASW', 'HG02479': 'ACB', 'HG02692': 'PJL', 'HG02491': 'PJL', 'NA18748': 'CHB', 'NA20806': 'TSI', 'HG00475': 'CHS', 'NA21100': 'GIH', 'NA19436': 'LWK', 'NA10845': 'CEU', 'NA20772': 'TSI', 'HG02079': 'KHV', 'HG00330': 'FIN', 'HG02398': 'CDX', 'NA18983': 'JPT', 'HG01631': 'IBS', 'HG01510': 'IBS', 'HG03199': 'ESN', 'HG01681': 'IBS', 'HG01550': 'CLM', 'NA20895': 'GIH', 'NA12827': 'CEU', 'HG02605': 'PJL', 'HG03196': 'ESN', 'NA12751': 'CEU', 'HG02252': 'PEL', 'HG03842': 'STU', 'HG04200': 'ITU', 'HG03846': 'STU', 'NA19774': 'MXL', 'HG02715': 'GWD', 'NA19705': 'ASW', 'HG03797': 'BEB', 'HG03618': 'PJL', 'NA20849': 'GIH', 'HG01878': 'KHV', 'HG03433': 'MSL', 'NA19797': 'MXL', 'HG00480': 'CHS', 'HG02276': 'PEL', 'HG01971': 'PEL', 'HG03635': 'PJL', 'NA18954': 'JPT', 'HG03651': 'PJL', 'NA10851': 'CEU', 'NA18519': 'YRI', 'NA19759': 'MXL', 'NA20515': 'TSI', 'HG03746': 'STU', 'NA10860': 'CEU', 'HG01809': 'CDX', 'HG00251': 'GBR', 'HG02567': 'GWD', 'HG01088': 'PUR', 'HG01484': 'CLM', 'NA19658': 'MXL', 'NA19174': 'YRI', 'HG04235': 'ITU', 'HG01694': 'IBS', 'HG03761': 'PJL', 'HG04155': 'BEB', 'HG01982': 'PEL', 'HG00642': 'PUR', 'HG03040': 'GWD', 'NA12155': 'CEU', 'HG01920': 'PEL', 'HG02219': 'IBS', 'NA11933': 'CEU', 'HG03371': 'ESN', 'HG03472': 'MSL', 'NA20807': 'TSI', 'NA21128': 'GIH', 'HG01459': 'CLM', 'NA20507': 'TSI', 'HG03549': 'MSL', 'HG02644': 'GWD', 'NA18986': 'JPT', 'NA18532': 'CHB', 'NA18642': 'CHB', 'NA19204': 'YRI', 'HG00635': 'CHS', 'HG02025': 'KHV', 'NA18507': 'YRI', 'HG00267': 'FIN', 'HG01415': 'PUR', 'NA21116': 'GIH', 'HG02761': 'GWD', 'HG01892': 'PEL', 'NA18561': 'CHB', 'HG01843': 'KHV', 'HG01526': 'IBS', 'HG02869': 'GWD', 'HG00122': 'GBR', 'HG02820': 'GWD', 'HG03133': 'ESN', 'HG02179': 'CDX', 'HG02260': 'PEL', 'HG01457': 'CLM', 'HG00326': 'FIN', 'NA12829': 'CEU', 'HG01704': 'IBS', 'NA19003': 'JPT', 'NA18570': 'CHB', 'HG03709': 'PJL', 'HG01871': 'KHV', 'HG03939': 'BEB', 'HG03594': 'BEB', 'HG02391': 'CDX', 'HG02429': 'ACB', 'HG00629': 'CHS', 'NA18537': 'CHB', 'HG00238': 'GBR', 'HG01705': 'IBS', 'NA18740': 'CHB', 'HG01799': 'CDX', 'HG01249': 'PUR', 'HG01490': 'CLM', 'NA19004': 'JPT', 'HG02140': 'KHV', 'HG03584': 'MSL', 'HG03714': 'ITU', 'NA07346': 'CEU', 'NA19373': 'LWK', 'HG00663': 'CHS', 'NA20864': 'GIH', 'NA20287': 'ASW', 'HG04038': 'STU', 'NA21102': 'GIH', 'HG03200': 'ESN', 'HG00130': 'GBR', 'HG02603': 'PJL', 'HG00281': 'FIN', 'NA18624': 'CHB', 'HG02525': 'KHV', 'HG00694': 'CHS', 'HG00636': 'CHS', ...}
a = {'Korea': 90, 'English': 100}
sample_dict.get('HG02276--', np.nan)
nan
matrix['Population'] = matrix.apply(
lambda r: sample_dict.get(r.name.split()[0], np.nan), axis=1)
matrix
0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | ... | 4991 | 4992 | 4993 | 4994 | 4995 | 4996 | 4997 | 4998 | 4999 | Population | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
HG00098 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00100 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00106 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
HG00112 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00114 num | NaN | NaN | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
HG00116 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 2.0 | 0.0 | GBR |
HG00117 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00118 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00119 num | NaN | NaN | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 | GBR |
HG00120 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
HG00122 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00123 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00124 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00126 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00131 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 | GBR |
HG00141 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00142 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 1.0 | GBR |
HG00143 num | NaN | NaN | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00144 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00145 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00146 num | NaN | NaN | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
HG00147 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00148 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
HG00149 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 1.0 | GBR |
HG00150 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 1.0 | GBR |
HG00151 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00152 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
HG00153 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
HG00156 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 | GBR |
HG00158 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
NA20786 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | TSI |
NA20787 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20790 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20792 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20795 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 2.0 | 1.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | TSI |
NA20796 num | NaN | NaN | 0.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20797 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20798 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 0.0 | 0.0 | TSI |
NA20799 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20800 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 0.0 | 0.0 | TSI |
NA20801 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20802 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20803 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 1.0 | 0.0 | TSI |
NA20804 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20805 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20806 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 | TSI |
NA20807 num | NaN | NaN | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | TSI |
NA20808 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20809 num | NaN | NaN | 1.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 0.0 | 0.0 | TSI |
NA20810 num | NaN | NaN | 2.0 | 2.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 2.0 | ... | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 0.0 | 0.0 | TSI |
NA20811 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20812 num | NaN | NaN | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20813 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20814 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 | TSI |
NA20815 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20816 num | NaN | NaN | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20818 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 2.0 | 0.0 | TSI |
NA20819 num | NaN | NaN | 1.0 | 2.0 | 1.0 | 0.0 | 0.0 | 1.0 | NaN | 2.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20826 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | TSI |
NA20828 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
629 rows × 5001 columns
from sklearn.preprocessing import StandardScaler
from sklearn.decomposition import PCA
from cycler import cycler
def get_pca_df(x):
x_std = StandardScaler().fit_transform(x)
pca = PCA(n_components=2)
y = pca.fit_transform(x_std)
pca_df = pd.DataFrame(y)
pca_df.index = x.index
pca_df.columns = ['C1', 'C2']
pca_df = pd.concat([x, pca_df], axis=1)
return pca_df
def draw_groups(groups, loc=None):
fig, ax = plt.subplots(figsize=(12,10))
colors = pd.tools.plotting._get_standard_colors(len(groups), color_type='random')
ax.set_prop_cycle(cycler('color', colors))
ax.margins(0.15)
for name, group in groups:
ax.plot(group['C1'], group['C2'], marker='o', linestyle='', ms=8, label=name)
ax.legend(numpoints=1, loc=loc)
matrix.ix[:,:-1].dropna(1)
2 | 3 | 5 | 7 | 9 | 12 | 13 | 14 | 16 | 17 | ... | 4988 | 4989 | 4990 | 4991 | 4992 | 4993 | 4995 | 4997 | 4998 | 4999 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
HG00098 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00100 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00106 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 |
HG00112 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00114 num | 1.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 |
HG00116 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 1.0 | 2.0 | 1.0 | 1.0 | 0.0 | 0.0 | 1.0 | 2.0 | 0.0 |
HG00117 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00118 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 1.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00119 num | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 |
HG00120 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 2.0 | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 |
HG00122 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00123 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00124 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00126 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00131 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 |
HG00141 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 1.0 | 2.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00142 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | ... | 1.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 |
HG00143 num | 1.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00144 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00145 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00146 num | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 1.0 | 2.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 |
HG00147 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00148 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 |
HG00149 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 |
HG00150 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 |
HG00151 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
HG00152 num | 0.0 | 1.0 | 0.0 | 1.0 | 1.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 |
HG00153 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 |
HG00156 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 |
HG00158 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 1.0 | 2.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
NA20786 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 |
NA20787 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20790 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20792 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20795 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 2.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 |
NA20796 num | 0.0 | 2.0 | 0.0 | 0.0 | 1.0 | 0.0 | 1.0 | 2.0 | 2.0 | 2.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20797 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20798 num | 0.0 | 1.0 | 0.0 | 1.0 | 1.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 |
NA20799 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20800 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 |
NA20801 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20802 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | ... | 0.0 | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20803 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 0.0 |
NA20804 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20805 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20806 num | 0.0 | 1.0 | 0.0 | 1.0 | 1.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 |
NA20807 num | 1.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 2.0 | ... | 0.0 | 2.0 | 2.0 | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 |
NA20808 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20809 num | 1.0 | 2.0 | 0.0 | 0.0 | 1.0 | 0.0 | 1.0 | 2.0 | 2.0 | 2.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 |
NA20810 num | 2.0 | 2.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 2.0 | 2.0 | 2.0 | ... | 0.0 | 0.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 |
NA20811 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 2.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20812 num | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20813 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20814 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 |
NA20815 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 1.0 | 2.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20816 num | 1.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 2.0 | ... | 0.0 | 2.0 | 2.0 | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20818 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | ... | 0.0 | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 0.0 |
NA20819 num | 1.0 | 2.0 | 0.0 | 1.0 | 2.0 | 0.0 | 1.0 | 2.0 | 2.0 | 2.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
NA20826 num | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 |
NA20828 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
629 rows × 2827 columns
pca_df = get_pca_df(matrix.ix[:,:-1].dropna(1))
pca_df['Population'] = matrix['Population']
draw_groups(pca_df.groupby('Population'), 'upper right')
matrix
0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | ... | 4991 | 4992 | 4993 | 4994 | 4995 | 4996 | 4997 | 4998 | 4999 | Population | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
HG00098 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00100 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00106 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
HG00112 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00114 num | NaN | NaN | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
HG00116 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 2.0 | 0.0 | GBR |
HG00117 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00118 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00119 num | NaN | NaN | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 | GBR |
HG00120 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
HG00122 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00123 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00124 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00126 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00131 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 | GBR |
HG00141 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00142 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 1.0 | GBR |
HG00143 num | NaN | NaN | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00144 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00145 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00146 num | NaN | NaN | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
HG00147 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00148 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
HG00149 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 1.0 | GBR |
HG00150 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 1.0 | GBR |
HG00151 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | GBR |
HG00152 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
HG00153 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
HG00156 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 | GBR |
HG00158 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | GBR |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
NA20786 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | TSI |
NA20787 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20790 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20792 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20795 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 2.0 | 1.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | TSI |
NA20796 num | NaN | NaN | 0.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20797 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20798 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 0.0 | 0.0 | TSI |
NA20799 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20800 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 0.0 | 0.0 | TSI |
NA20801 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20802 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20803 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 1.0 | 0.0 | TSI |
NA20804 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20805 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20806 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 | TSI |
NA20807 num | NaN | NaN | 1.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | TSI |
NA20808 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20809 num | NaN | NaN | 1.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 0.0 | 0.0 | TSI |
NA20810 num | NaN | NaN | 2.0 | 2.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 2.0 | ... | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | 0.0 | 0.0 | TSI |
NA20811 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20812 num | NaN | NaN | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20813 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20814 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 1.0 | TSI |
NA20815 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20816 num | NaN | NaN | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20818 num | NaN | NaN | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 2.0 | 0.0 | TSI |
NA20819 num | NaN | NaN | 1.0 | 2.0 | 1.0 | 0.0 | 0.0 | 1.0 | NaN | 2.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
NA20826 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 1.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 1.0 | 0.0 | TSI |
NA20828 num | NaN | NaN | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | ... | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | NaN | 0.0 | 0.0 | 0.0 | TSI |
629 rows × 5001 columns
matrix2 = matrix.dropna(1)
ceu = matrix2[matrix2['Population'] == 'CEU']
chb = matrix2[matrix2['Population'] == 'CHB']
ceu_ids = list(ceu.index)
chb_ids = list(chb.index)
matrix2
2 | 3 | 5 | 7 | 9 | 12 | 13 | 14 | 16 | 17 | ... | 4989 | 4990 | 4991 | 4992 | 4993 | 4995 | 4997 | 4998 | 4999 | Population | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
HG00098 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00100 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00106 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | GBR |
HG00112 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00114 num | 1.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | ... | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | GBR |
HG00116 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 1.0 | 2.0 | 1.0 | 1.0 | 0.0 | 0.0 | 1.0 | 2.0 | 0.0 | GBR |
HG00117 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00118 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 1.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00119 num | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | GBR |
HG00120 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 2.0 | 2.0 | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | GBR |
HG00122 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00123 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00124 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00126 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00131 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | GBR |
HG00141 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 1.0 | 2.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00142 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | GBR |
HG00143 num | 1.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00144 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00145 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00146 num | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | ... | 1.0 | 2.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | GBR |
HG00147 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00148 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | GBR |
HG00149 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | GBR |
HG00150 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | GBR |
HG00151 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | GBR |
HG00152 num | 0.0 | 1.0 | 0.0 | 1.0 | 1.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | GBR |
HG00153 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | GBR |
HG00156 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | GBR |
HG00158 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 1.0 | 2.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | GBR |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
NA20786 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | TSI |
NA20787 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20790 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20792 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20795 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 2.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | TSI |
NA20796 num | 0.0 | 2.0 | 0.0 | 0.0 | 1.0 | 0.0 | 1.0 | 2.0 | 2.0 | 2.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20797 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20798 num | 0.0 | 1.0 | 0.0 | 1.0 | 1.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | TSI |
NA20799 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20800 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | TSI |
NA20801 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20802 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | ... | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20803 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 2.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 0.0 | TSI |
NA20804 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20805 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20806 num | 0.0 | 1.0 | 0.0 | 1.0 | 1.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 2.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | TSI |
NA20807 num | 1.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 2.0 | ... | 2.0 | 2.0 | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | TSI |
NA20808 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20809 num | 1.0 | 2.0 | 0.0 | 0.0 | 1.0 | 0.0 | 1.0 | 2.0 | 2.0 | 2.0 | ... | 0.0 | 2.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | TSI |
NA20810 num | 2.0 | 2.0 | 0.0 | 0.0 | 2.0 | 0.0 | 0.0 | 2.0 | 2.0 | 2.0 | ... | 0.0 | 2.0 | 1.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | TSI |
NA20811 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 2.0 | ... | 0.0 | 2.0 | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20812 num | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20813 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | ... | 0.0 | 2.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20814 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | TSI |
NA20815 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | ... | 1.0 | 2.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20816 num | 1.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 2.0 | ... | 2.0 | 2.0 | 0.0 | 1.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20818 num | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | ... | 1.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 2.0 | 0.0 | TSI |
NA20819 num | 1.0 | 2.0 | 0.0 | 1.0 | 2.0 | 0.0 | 1.0 | 2.0 | 2.0 | 2.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
NA20826 num | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 0.0 | TSI |
NA20828 num | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 1.0 | 1.0 | ... | 0.0 | 2.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | TSI |
629 rows × 2828 columns
def get_ttest_pvalue(s):
try:
x1 = list(s[ceu_ids])
x2 = list(s[chb_ids])
if not x1 or not x2:
return np.nan
return stats.ttest_ind(x1, x2)[1]
except:
return np.nan
matrix2.apply(get_ttest_pvalue)
/usr/local/lib/python3.5/site-packages/scipy/stats/stats.py:249: RuntimeWarning: The input array could not be properly checked for nan values. nan values will be ignored. "values. nan values will be ignored.", RuntimeWarning)
2 3.001240e-01 3 5.077094e-10 5 4.455631e-02 7 4.395198e-01 9 8.239539e-02 12 1.957032e-02 13 9.170527e-02 14 1.132260e-02 16 1.626908e-02 17 7.837922e-02 20 2.717679e-03 22 1.749647e-03 23 4.161932e-03 26 7.064017e-03 27 8.737629e-03 28 9.362104e-03 29 1.749647e-03 30 1.749647e-03 32 2.101233e-01 34 2.717679e-03 40 1.110325e-03 42 2.717679e-03 49 4.072045e-01 55 3.639410e-03 59 8.399446e-03 61 1.221159e-01 62 4.455631e-02 64 4.404638e-01 66 1.208496e-01 67 NaN ... 4966 5.805121e-04 4967 4.568664e-03 4968 5.023331e-05 4969 7.493982e-01 4970 6.569898e-02 4971 1.413589e-02 4972 9.131017e-02 4973 3.059390e-01 4975 3.121692e-03 4977 1.028203e-01 4978 9.459553e-03 4979 NaN 4980 1.952565e-01 4981 3.024057e-01 4982 8.373549e-03 4983 3.364626e-01 4985 3.869401e-03 4986 2.512300e-01 4987 2.254631e-02 4988 1.957032e-02 4989 1.893101e-01 4990 2.185872e-01 4991 2.113554e-01 4992 4.729785e-02 4993 1.028203e-01 4995 NaN 4997 8.821178e-02 4998 4.157188e-01 4999 3.026712e-02 Population NaN dtype: float64