What are the most important genome/SNP/SNPedia sites to query from a VCF file of one's genome? How do I visualize my genomic data

Alex K Chen · October 4, 2023

https://knausb.github.io/vcfR_documentation/visualization_2.html

These aren't the **most** critical, but there are some variants for plasmalogens, some variants for how well one digests kimchi, COMT variants, etc..

There are some FOXO variants:

https://www.rapamycin.news/t/just-dna-seq-open-source-longevity-genetics-generator-see-your-oakvar-report-of-your-genomic-longevity-variants/4481/3 (this is so preliminary it's hard to interpret, there is no way in hell my PRS risk score is 92%).

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for nebula sequencing they use this as reference file: ##reference=file:///mnt/ssd/MegaBOLT_scheduler/reference/hg38.fa

here are some example variants on maybe more actionable things (like methylation):

Quote

I am taking Prodrome Glia for white matter inflammation issues derived from Lyme Disease. I haven’t found a single thread discussing Dayans work other than this. So please keep the discussion going.

I suspect my issue is that I have several genetic variants that might be contributing:

rs7946 T/T:

PEMT pathway is responsible for the body’s production of phosphatidylcholine, which is part of the phospholipid bilayer making up the membranes surrounding our cells. The PEMT enzyme is key in the body’s ability to create choline. Genetic variants that decrease the function of the enzyme cause greater reliance on choline from dietary sources.

rs10791957:
> - A/C: reduced turnover of methionine to phosphatidylcholine

Plus:

rs18J01133: >- A/G: one copy of **MTHFR C677T** allele, enzyme function decreased by 40%

Haven’t tested my father on prodrome (yet), but for me, I tested on the 2nd percentile for Total PhosphatidylCholine at age 32 and with a healthy diet. After 3 months of taking 10g a day of Sunflower lecithin I only went up of the 12th percentile. So I am taking now PC capsules in addition. Will test again soon and share my results.

my MTHFR variants (only for regulatory variants, this does not contain 1298 A>C (rs1801131)😞

Quote

chr1    11791061        rs7518348       A       G       656.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=28.56;SOR=1.270;VQSLOD=6.39;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,23:24:69:685,69,0
chr1    11791893        rs6700268       C       G       1397.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=53;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=26.37;SOR=1.654;VQSLOD=4.40;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,53:53:99:1426,156,0
chr1    11792912        rs4846050       T       C       955.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.87;SOR=1.179;VQSLOD=7.11;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,32:33:96:984,96,0
chr1    11793149        rs5772477       C       CT      291.74 PASS    AC=2;AF=1.00;AN=2;DB;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=29.17;SOR=1.085;VQSLOD=3.91;culprit=FS GT:AD:DP:GQ:PL 1/1:0,10:10:30:329,30,0
chr1    11793450        rs542060620     CTTTTTTTTTTTT   C       887.73 PASS    AC=2;AF=1.00;AN=2;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=27.39;SOR=1.828;VQSLOD=3.89;culprit=FS GT:AD:DP:GQ:PL 1/1:0,21:21:63:925,63,0
chr1    11793542        rs7535669       G       C       997.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=33.26;SOR=0.976;VQSLOD=7.44;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,30:30:89:1026,89,0
chr1    11794400        rs4846051       G       A       1567.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=32.14;SOR=1.005;VQSLOD=7.28;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,42:42:99:1596,126,0
chr1    11794698        rs1994798       G       A       1393.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=35.10;SOR=0.693;VQSLOD=7.19;culprit=QD      GT:AD:DP:GQ:PL 1/1:0,38:38:99:1422,114,0
chr1    11795810        rs6541003       G       A       1436.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=32.12;SOR=1.061;VQSLOD=7.28;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,36:36:99:1465,108,0
chr1    11796321        rs1801133       G       A       561.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.712;DB;DP=39;ExcessHet=3.0103;FS=1.243;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.40;ReadPosRankSum=-1.307e+00;SOR=1.022;VQSLOD=4.03;culprit=FS   GT:AD:DP:GQ:PL 0/1:20,19:39:99:590,0,616
chr1    11796764        rs7545331       G       C       1705.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=34.12;SOR=0.952;VQSLOD=6.73;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,50:50:99:1734,149,0
chr1    11797183        rs7526128       C       T       668.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=32.00;SOR=1.402;VQSLOD=5.01;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,19:20:57:697,57,0
chr1    11797196        rs1323763550    CAA     C       555.73 PASS    AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=36.56;SOR=1.112;VQSLOD=3.54;culprit=QD GT:AD:DP:GQ:PL 1/1:0,14:15:42:593,42,0
chr1    11797324        rs6541004       T       C       1073.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=32.54;SOR=1.542;VQSLOD=5.60;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,33:33:98:1102,98,0
chr1    11797353        rs7537955       A       G       1384.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=27.18;SOR=2.133;VQSLOD=5.81;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,39:39:99:1413,117,0
chr1    11797468        rs6541005       A       T       1629.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=35.20;SOR=0.798;VQSLOD=6.53;culprit=QD      GT:AD:DP:GQ:PL 1/1:0,37:38:99:1658,111,0
chr1    11797469        rs6541006       A       T       1771.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=28.16;SOR=0.798;VQSLOD=4.88;culprit=FS GT:AD:DP:GQ:PL 1/1:0,37:38:99:1800,120,0
chr1    11797894        rs4846052       T       C       1172.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=27.92;SOR=0.788;VQSLOD=6.44;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,42:42:99:1201,124,0
chr1    11798615        rs4845885       T       C       1176.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=27.37;SOR=1.312;VQSLOD=5.57;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,43:43:99:1205,128,0
chr1    11799852        rs7527897       A       G       951.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.74;SOR=0.957;VQSLOD=6.64;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,32:32:96:980,96,0
chr1    11800063        rs11121832      T       C       946.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=27.05;SOR=1.002;VQSLOD=6.57;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,35:35:99:975,104,0
chr1    11800626        rs7533315       T       C       1065.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.60;SOR=1.061;VQSLOD=6.77;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,36:36:99:1094,108,0
chr1    11801923        rs200892006     CAAAAAAAAAAAAA C       1043.73 PASS    AC=2;AF=1.00;AN=2;DB;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=28.11;SOR=1.051;VQSLOD=5.57;culprit=FS GT:AD:DP:GQ:PL 1/1:0,24:24:73:1081,73,0
chr1    11802157        rs9651118       T       C       566.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-2.869e+00;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=15.74;ReadPosRankSum=-1.284e+00;SOR=0.703;VQSLOD=5.44;culprit=FS      GT:AD:DP:GQ:PL 0/1:17,19:36:99:595,0,585
chr10   11791026        rs6602533       T       C       1114.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=30.97;SOR=1.209;VQSLOD=6.78;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,36:36:99:1143,107,0
chr10   11792003        rs35420609      C       A       581.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.23;DB;DP=43;ExcessHet=3.0103;FS=4.506;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=13.85;ReadPosRankSum=0.933;SOR=0.954;VQSLOD=1.78;culprit=ReadPosRankSum     GT:AD:DP:GQ:PL 0/1:22,20:42:99:610,0,674
chr10   11792352        rs17554109      G       A       430.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=3.28;DB;DP=30;ExcessHet=3.0103;FS=8.557;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=15.95;ReadPosRankSum=-1.274e+00;SOR=1.000;VQSLOD=2.19;culprit=FS    GT:AD:DP:GQ:PL 0/1:13,14:29:99:459,0,294
chr10   11792872        rs764165007     TGAG    T       499.73 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.30;DB;DP=33;ExcessHet=3.0103;FS=8.139;MLEAC=1;MLEAF=0.500;MQRankSum=-1.320e+00;QD=16.12;ReadPosRankSum=0.414;SOR=0.120;VQSLOD=0.797;culprit=FS      GT:AD:DP:GQ:PGT:PID:PL:PS       0|1:17,14:31:99:0|1:11792872_TGAG_T:537,0,672:11792872
chr10   11792877        rs75620717      G       T       508.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.17;DB;DP=31;ExcessHet=3.0103;FS=8.139;MLEAC=1;MLEAF=0.500;MQRankSum=-1.320e+00;QD=16.41;ReadPosRankSum=1.01;SOR=0.120;VQSLOD=0.790;culprit=SOR      GT:AD:DP:GQ:PGT:PID:PL:PS       0|1:17,14:31:99:0|1:11792872_TGAG_T:537,0,672:11792872
chr10   11792880        rs762076012     C       CCAG    571.73 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-8.830e-01;DB;DP=33;ExcessHet=3.0103;FS=8.039;MLEAC=1;MLEAF=0.500;MQRankSum=-1.081e+00;QD=17.33;ReadPosRankSum=0.661;SOR=0.120;VQSLOD=0.780;culprit=FS        GT:AD:DP:GQ:PGT:PID:PL:PS       0|1:17,16:33:99:0|1:11792872_TGAG_T:609,0,666:11792872
chr10   11792882        rs78887114      C       T       580.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.11;DB;DP=34;ExcessHet=3.0103;FS=8.039;MLEAC=1;MLEAF=0.500;MQRankSum=-1.081e+00;QD=17.60;ReadPosRankSum=0.090;SOR=0.120;VQSLOD=1.42;culprit=SOR      GT:AD:DP:GQ:PGT:PID:PL:PS       0|1:17,16:33:99:0|1:11792872_TGAG_T:609,0,666:11792872
chr10   11792941        rs4750114       C       G       1327.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=27.48;SOR=1.432;VQSLOD=4.50;culprit=FS GT:AD:DP:GQ:PL 1/1:0,37:37:99:1356,110,0
chr10   11792969        rs4750115       A       G       391.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-3.952e+00;DB;DP=40;ExcessHet=3.0103;FS=4.649;MLEAC=1;MLEAF=0.500;MQRankSum=0.583;QD=10.05;ReadPosRankSum=-9.070e-01;SOR=1.473;VQSLOD=0.247;culprit=QD        GT:AD:DP:GQ:PL 0/1:22,17:39:99:420,0,770
chr10   11793513        rs7915245       C       T       1231.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=35.23;SOR=1.688;VQSLOD=4.77;culprit=QD      GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,28:29:84:1|1:11793513_C_T:1260,84,0:11793513
chr10   11793515        rs7903322       T       C       1231.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=31.95;SOR=1.688;VQSLOD=4.22;culprit=FS GT:AD:DP:GQ:PGT:PID:PL:PS       1|1:0,28:29:84:1|1:11793513_C_T:1260,84,0:11793513
chr10   11793661        rs201820594     TTTTTCTTTTCTTTTCTTTTCTTTTC      T       116.73 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-1.282e+00;DB;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=19.46;ReadPosRankSum=-1.834e+00;SOR=0.693;VQSLOD=2.26;culprit=FS GT:AD:DP:GQ:PL 0/1:2,4:6:71:154,0,71
chr10   11795657        rs7910181       C       T       187.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.275;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=18.78;ReadPosRankSum=-6.480e-01;SOR=0.569;VQSLOD=2.49;culprit=FS       GT:AD:DP:GQ:PL 0/1:3,7:10:84:216,0,84
chr10   11795825        rs4750119       G       A       1293.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=31.07;SOR=2.833;VQSLOD=5.59;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,33:33:99:1322,99,0
chr10   11796224        rs1310693610    C       CA      227.74 PASS    AC=2;AF=1.00;AN=2;DB;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=25.30;SOR=0.892;VQSLOD=3.72;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,9:9:27:265,27,0
chr10   11796401        rs11257329      T       C       423.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-4.224e+00;DB;DP=30;ExcessHet=3.0103;FS=3.890;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.61;ReadPosRankSum=-1.465e+00;SOR=0.198;VQSLOD=3.85;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:12,17:29:99:452,0,392
chr10   11796670        rs6602534       T       C       982.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=30.71;SOR=0.818;VQSLOD=7.17;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,32:32:96:1011,96,0
chr10   11797031        rs10906019      T       A       218.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-4.480e-01;DB;DP=30;ExcessHet=3.0103;FS=1.657;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=8.41;ReadPosRankSum=-6.690e-01;SOR=1.402;VQSLOD=1.62;culprit=QD       GT:AD:DP:GQ:PL 0/1:18,8:27:99:247,0,633
chr10   11797191        rs6602535       C       T       1183.77 PASS    AC=2;AF=1.00;AN=2;BaseQRankSum=1.76;DB;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=29.68;ReadPosRankSum=0.00;SOR=0.307;VQSLOD=6.52;culprit=FS    GT:AD:DP:GQ:PL 1/1:1,31:32:86:1212,86,0
chr10   11798499        rs7908067       A       C       747.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.91;SOR=1.022;VQSLOD=6.50;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,25:26:73:776,73,0
chr10   11800133        rs3889052       C       A       920.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=36.61;SOR=1.519;VQSLOD=5.14;culprit=QD      GT:AD:DP:GQ:PL 1/1:0,24:24:72:949,72,0
chr10   11800226        rs1424133015    CT      C       102.90 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=17.15;ReadPosRankSum=-6.740e-01;SOR=0.368;VQSLOD=3.75;culprit=FS     GT:AD:DP:GQ:PL 0/1:1,5:6:14:140,0,14
chr10   11800290        rs4356136       G       T       302.78 PASS    AC=2;AF=1.00;AN=2;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.67;SOR=1.179;VQSLOD=3.89;culprit=FS       GT:AD:DP:GQ:PL 1/1:0,8:8:24:331,24,0
chr10   11800954        rs1815306       C       T       1171.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=27.50;SOR=0.941;VQSLOD=6.67;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,33:34:98:1200,98,0
chr10   11801052        rs942530        C       T       1400.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.12;SOR=0.746;VQSLOD=7.10;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,36:37:99:1429,108,0
chr10   11801410        rs201612497     CTTTTTTTTT      C       1775.73 PASS    AC=2;AF=1.00;AN=2;DB;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=30.66;SOR=1.005;VQSLOD=5.44;culprit=FS GT:AD:DP:GQ:PL 1/1:0,40:42:99:1813,126,0
chr10   11803011        rs6602537       T       C       998.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=31.21;SOR=0.818;VQSLOD=6.83;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,32:32:95:1027,95,0
chr10   11803059        rs6602538       T       C       1105.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.89;SOR=0.746;VQSLOD=6.33;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,37:37:99:1134,110,0
chr11   11791074        rs72854808      A       T       862.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=28.49;SOR=0.963;VQSLOD=6.22;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,23:23:75:891,75,0
chr11   11791516        rs7940345       T       C       855.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=28.53;SOR=0.826;VQSLOD=6.52;culprit=QD      GT:AD:DP:GQ:PL 1/1:0,30:30:90:884,90,0
chr11   11791797        rs7950577       G       A       1563.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=45;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=36.69;SOR=0.990;VQSLOD=6.58;culprit=QD      GT:AD:DP:GQ:PL 1/1:0,44:44:99:1592,131,0
chr11   11792346        rs11022038      A       T       1400.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=25.02;SOR=1.179;VQSLOD=5.66;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,38:38:99:1429,114,0
chr11   11792467        rs376301547     T       C       385.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-2.848e+00;DB;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=15.43;ReadPosRankSum=1.38;SOR=0.839;VQSLOD=3.87;culprit=FS        GT:AD:DP:GQ:PL 0/1:9,16:26:99:414,0,266
chr11   11792629        rs16910148      C       T       1429.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.45;SOR=0.693;VQSLOD=7.19;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,36:36:99:1458,108,0
chr11   11793154        rs16910152      T       G       1119.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=31.10;SOR=1.371;VQSLOD=6.13;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,36:36:99:1148,107,0
chr11   11793613        rs150690263     AAAATT A       1782.73 PASS    AC=2;AF=1.00;AN=2;DB;DP=48;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.73;SOR=1.179;VQSLOD=6.51;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,41:43:99:1820,124,0
chr11   11794746        rs10831674      A       T       1182.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=28.95;SOR=0.693;VQSLOD=6.52;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,32:34:96:1211,96,0
chr11   11796517        rs16910159      G       A       625.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=19;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.04;SOR=0.804;VQSLOD=5.26;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,17:17:51:654,51,0
chr11   11797187        rs113190524     C       T       1743.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=27.56;SOR=1.426;VQSLOD=3.92;culprit=FS GT:AD:DP:GQ:PL 1/1:0,46:48:99:1772,138,0
chr11   11797340        rs144215882     G       C       1716.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=25.18;SOR=1.203;VQSLOD=4.42;culprit=FS GT:AD:DP:GQ:PL 1/1:0,45:46:99:1745,135,0
chr11   11798902        rs10831676      A       C       977.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=33.72;SOR=1.071;VQSLOD=7.07;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,29:29:86:1006,86,0
chr11   11799086        rs10765888      A       G       1257.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=32.90;SOR=1.085;VQSLOD=7.66;culprit=QD      GT:AD:DP:GQ:PL 1/1:0,34:34:99:1286,102,0
chr11   11801491        rs4910421       C       G       1030.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=30;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=27.93;SOR=1.255;VQSLOD=6.15;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,29:29:87:1059,87,0
chr11   11801735        rs369035976     G       C       411.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-8.590e-01;DB;DP=33;ExcessHet=3.0103;FS=3.180;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=13.28;ReadPosRankSum=-6.550e-01;SOR=0.293;VQSLOD=2.37;culprit=SOR GT:AD:DP:GQ:PL 0/1:17,14:31:99:440,0,519
chr11   11802003        rs7120452       C       T       1460.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=32.73;SOR=1.179;VQSLOD=7.04;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,38:38:99:1489,114,0
chr11   11802708        rs1380144972    AT      A       887.73 PASS    AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=32.64;SOR=1.230;VQSLOD=5.14;culprit=FS GT:AD:DP:GQ:PGT:PID:PL:PS       1|1:0,21:21:63:1|1:11802708_AT_A:925,63,0:11802708
chr11   11802727        rs7123478       G       T       1054.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=25;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=30.78;SOR=1.136;VQSLOD=4.74;culprit=FS GT:AD:DP:GQ:PGT:PID:PL:PS       1|1:0,25:25:75:1|1:11802708_AT_A:1083,75,0:11802708
chr12   11791178        rs2724624       T       A       1019.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=26.33;SOR=0.846;VQSLOD=6.35;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,26:26:78:1048,78,0
chr12   11791291        rs2856332       C       T       1291.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=34;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=36.54;SOR=0.811;VQSLOD=7.32;culprit=QD      GT:AD:DP:GQ:PL 1/1:0,34:34:99:1320,102,0
chr12   11791394        rs762718        A       G       421.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-2.033e+00;DB;DP=31;ExcessHet=3.0103;FS=1.412;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=13.61;ReadPosRankSum=1.13;SOR=1.112;VQSLOD=3.99;culprit=ReadPosRankSum        GT:AD:DP:GQ:PL 0/1:16,15:31:99:450,0,555
chr12   11791542        rs2723824       G       C       1435.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=24.69;SOR=0.914;VQSLOD=5.14;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,38:38:99:1464,114,0
chr12   11791756        rs5796467       A       ATGT    1702.73 PASS    AC=2;AF=1.00;AN=2;DB;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=28.71;SOR=1.236;VQSLOD=6.00;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,39:39:99:1740,117,0
chr12   11791772        rs2710283       T       G       1254.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=33.02;SOR=0.798;VQSLOD=6.70;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,38:38:99:1283,113,0
chr12   11791918        rs2724623       G       C       1814.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=51;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=32.31;SOR=0.909;VQSLOD=5.94;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,48:49:99:1843,144,0
chr12   11791976        rs2710282       T       C       1400.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=47;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=31.13;SOR=0.874;VQSLOD=5.75;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,45:46:99:1429,134,0
chr12   11792145        rs2710281       T       C       1031.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.48;SOR=0.804;VQSLOD=5.49;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,35:36:99:1060,104,0
chr12   11792326        rs2723823       T       C       1181.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=26.36;SOR=1.061;VQSLOD=6.73;culprit=QD      GT:AD:DP:GQ:PL 1/1:0,33:36:99:1210,99,0
chr12   11792686        rs5796468       C       CA      443.82 PASS    AC=2;AF=1.00;AN=2;BaseQRankSum=-1.424e+00;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=26.11;ReadPosRankSum=0.773;SOR=0.551;VQSLOD=3.46;culprit=FS     GT:AD:DP:GQ:PL 1/1:1,16:18:17:481,17,0
chr12   11793018        rs2724622       A       C       1218.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=32.94;SOR=0.859;VQSLOD=7.67;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,37:37:99:1247,110,0
chr12   11795015        rs2710280       T       G       1672.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=33.38;SOR=1.067;VQSLOD=6.84;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,46:48:99:1701,138,0
chr12   11796185        rs71981297      TGTGA   T       1762.73 PASS    AC=2;AF=1.00;AN=2;DB;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=31.56;SOR=1.151;VQSLOD=7.24;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,40:40:99:1800,121,0
chr12   11796779        rs35668980      T       TG      835.73 PASS    AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=27.70;SOR=1.085;VQSLOD=5.90;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,21:22:65:873,65,0
chr12   11797291        rs60795005      TC      T       2115.73 PASS    AC=2;AF=1.00;AN=2;DB;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=26.94;SOR=0.963;VQSLOD=5.64;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,48:48:99:2153,145,0
chr12   11798181        rs2724620       C       T       1185.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=28.35;SOR=0.756;VQSLOD=6.81;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,31:31:93:1214,93,0
chr12   11799490        rs762721        A       C       1099.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=36;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=31.42;SOR=1.148;VQSLOD=7.19;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,35:35:99:1128,105,0
chr12   11800969        rs2723840       C       G       1272.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=32.04;SOR=1.061;VQSLOD=7.00;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,36:36:99:1301,107,0
chr12   11801723        rs762722        C       G       1076.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=34.73;SOR=0.892;VQSLOD=7.39;culprit=QD      GT:AD:DP:GQ:PL 1/1:0,31:31:88:1105,88,0
chr16   11790688        rs8059377       C       A       649.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=3.57;DB;DP=39;ExcessHet=3.0103;FS=7.216;MLEAC=1;MLEAF=0.500;MQRankSum=-8.470e-01;POSITIVE_TRAIN_SITE;QD=17.10;ReadPosRankSum=0.059;SOR=1.397;VQSLOD=2.01;culprit=FS   GT:AD:DP:GQ:PL 0/1:17,21:38:99:678,0,361
chr16   11791587        rs72782733      C       A       260.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=3.10;DB;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=10.03;ReadPosRankSum=1.40;SOR=0.963;VQSLOD=4.63;culprit=FS GT:AD:DP:GQ:PL 0/1:17,9:26:99:289,0,516
chr16   11792735        rs6498245       A       G       1245.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=31.14;SOR=0.902;VQSLOD=7.58;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,40:40:99:1274,120,0
chr16   11793313        rs6498246       G       A       298.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.96;DB;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=9.96;ReadPosRankSum=-1.360e+00;SOR=0.693;VQSLOD=4.77;culprit=FS     GT:AD:DP:GQ:PL 0/1:19,11:31:99:327,0,478
chr16   11793532        rs550786318     C       CA      711.73 PASS    AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=33.89;SOR=3.816;VQSLOD=3.20;culprit=SOR     GT:AD:DP:GQ:PL 1/1:0,21:21:63:749,63,0
chr16   11793674        rs8056774       A       T       748.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-9.360e-01;DB;DP=30;ExcessHet=3.0103;FS=1.664;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=24.96;ReadPosRankSum=-3.750e-01;SOR=0.610;VQSLOD=1.64;culprit=QD      GT:AD:DP:GQ:PL 0/1:8,22:30:99:777,0,231
chr16   11793773        rs62038760      A       G       733.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-2.075e+00;DB;DP=39;ExcessHet=3.0103;FS=2.826;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=19.31;ReadPosRankSum=0.493;SOR=0.509;VQSLOD=3.60;culprit=FS   GT:AD:DP:GQ:PL 0/1:15,23:38:99:762,0,490
chr16   11793792        rs8061475       T       C       1466.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=33.53;SOR=0.793;VQSLOD=7.52;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,40:40:99:1495,120,0
chr16   11795063        rs8048397       C       T       383.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.31;DB;DP=23;ExcessHet=3.0103;FS=1.707;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=17.44;ReadPosRankSum=0.495;SOR=0.368;VQSLOD=3.09;culprit=FS GT:AD:DP:GQ:PL 0/1:10,12:22:99:412,0,311
chr16   11795203        rs8053548       T       C       212.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-3.116e+00;DB;DP=20;ExcessHet=3.0103;FS=4.534;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=11.20;ReadPosRankSum=-4.540e-01;SOR=0.435;VQSLOD=1.59;culprit=QD      GT:AD:DP:GQ:PL 0/1:8,11:19:99:241,0,266
chr16   11795236        rs11864383      G       C       235.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-4.720e-01;DB;DP=22;ExcessHet=3.0103;FS=4.123;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=11.23;ReadPosRankSum=-1.780e-01;SOR=1.288;VQSLOD=1.72;culprit=QD      GT:AD:DP:GQ:PL 0/1:12,9:21:99:264,0,408
chr16   11797059        rs755431804     C       CGG     121.73 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.07;DB;DP=7;ExcessHet=3.0103;FS=8.451;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=17.39;ReadPosRankSum=-8.420e-01;SOR=1.402;VQSLOD=-8.775e-01;culprit=FS   GT:AD:DP:GQ:PL 0/1:3,4:7:99:159,0,114
chr16   11797264        rs148383532     G       A       227.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.24;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=22.78;ReadPosRankSum=0.755;SOR=0.527;VQSLOD=2.17;culprit=FS     GT:AD:DP:GQ:PL 0/1:3,7:10:61:256,0,61
chr16   11797505        rs28495625      C       A       596.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.38;DB;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=19.25;ReadPosRankSum=-4.100e-02;SOR=0.473;VQSLOD=4.16;culprit=FS    GT:AD:DP:GQ:PL 0/1:11,20:31:99:625,0,304
chr16   11798194        rs3960407       A       G       414.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-2.010e-01;DB;DP=41;ExcessHet=3.0103;FS=4.831;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=10.37;ReadPosRankSum=0.224;SOR=1.545;VQSLOD=1.48;culprit=QD   GT:AD:DP:GQ:PL 0/1:25,15:40:99:443,0,827
chr16   11799021        rs566786090     C       CAAA    136.73 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.98;DB;DP=19;ExcessHet=3.0103;FS=2.077;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=8.04;ReadPosRankSum=-1.690e+00;SOR=0.850;VQSLOD=0.540;culprit=QD        GT:AD:DP:GQ:PL 0/1:12,5:17:99:174,0,445
chr16   11799663        rs891210        C       G       335.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.22;DB;DP=31;ExcessHet=3.0103;FS=8.700;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=11.19;ReadPosRankSum=-2.750e-01;SOR=1.261;VQSLOD=2.21;culprit=FS    GT:AD:DP:GQ:PL 0/1:18,12:30:99:364,0,594
chr16   11800064        rs8055639       G       T       418.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=3.50;DB;DP=27;ExcessHet=3.0103;FS=1.583;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=16.11;ReadPosRankSum=0.777;SOR=0.346;VQSLOD=3.79;culprit=FS GT:AD:DP:GQ:PL 0/1:13,13:27:99:447,0,375
chr16   11800198        rs2160184       A       T       478.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-3.700e-01;DB;DP=35;ExcessHet=3.0103;FS=7.319;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.08;ReadPosRankSum=0.639;SOR=1.541;VQSLOD=2.49;culprit=FS   GT:AD:DP:GQ:PL 0/1:18,16:34:99:507,0,615
chr16   11800358        rs2110620       T       C       1168.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=28.67;SOR=0.765;VQSLOD=5.86;culprit=FS      GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,27:27:81:1|1:11800358_T_C:1197,81,0:11800358
chr16   11800360        rs2110619       T       C       1168.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=25.80;SOR=0.765;VQSLOD=6.15;culprit=FS      GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,27:27:81:1|1:11800358_T_C:1197,81,0:11800358
chr16   11800859        rs56293020      T       C       1517.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=39;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=30.20;SOR=1.236;VQSLOD=5.44;culprit=FS GT:AD:DP:GQ:PGT:PID:PL:PS       1|1:0,38:39:99:1|1:11800859_T_C:1546,114,0:11800859
chr16   11800860        rs76419258      A       G       479.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-1.450e+00;DB;DP=39;ExcessHet=3.0103;FS=1.310;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=12.97;ReadPosRankSum=1.56;SOR=1.051;VQSLOD=2.43;culprit=FS        GT:AD:DP:GQ:PGT:PID:PL:PS       0|1:17,20:38:99:0|1:11800859_T_C:508,0,482:11800859
chr16   11801296        rs6498247       G       A       406.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.84;DB;DP=22;ExcessHet=3.0103;FS=4.359;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=20.34;ReadPosRankSum=1.07;SOR=0.132;VQSLOD=2.35;culprit=SOR GT:AD:DP:GQ:PGT:PID:PL:PS       0|1:9,11:21:99:0|1:11801296_G_A:435,0,343:11801296
chr16   11801298        rs6498248       G       A       406.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.76;DB;DP=21;ExcessHet=3.0103;FS=4.359;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=20.34;ReadPosRankSum=1.07;SOR=0.132;VQSLOD=2.34;culprit=SOR GT:AD:DP:GQ:PGT:PID:PL:PS       0|1:9,11:21:99:0|1:11801296_G_A:435,0,343:11801296
chr16   11801523        rs6498249       T       G       807.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=35.82;SOR=0.776;VQSLOD=5.78;culprit=QD      GT:AD:DP:GQ:PL 1/1:0,22:23:66:836,66,0
chr16   11801693        rs3905565       C       G       180.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.095;DB;DP=29;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=6.23;ReadPosRankSum=0.448;SOR=0.903;VQSLOD=4.52;culprit=QD GT:AD:DP:GQ:PL 0/1:20,9:29:99:209,0,618
chr16   11801707        rs7206424       C       G       209.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-6.220e-01;DB;DP=32;ExcessHet=3.0103;FS=1.607;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=6.99;ReadPosRankSum=-7.250e-01;SOR=1.274;VQSLOD=1.60;culprit=QD       GT:AD:DP:GQ:PL 0/1:21,9:30:99:238,0,706
chr16   11801785        rs12446699      C       T       653.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=3.68;DB;DP=29;ExcessHet=3.0103;FS=1.617;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=23.35;ReadPosRankSum=-1.378e+00;SOR=0.905;VQSLOD=2.55;culprit=FS    GT:AD:DP:GQ:PL 0/1:9,19:28:99:682,0,196
chr16   11802159        rs4538034       G       A       482.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.15;DB;DP=34;ExcessHet=3.0103;FS=1.377;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.20;ReadPosRankSum=-3.450e-01;SOR=1.218;VQSLOD=3.65;culprit=ReadPosRankSum        GT:AD:DP:GQ:PL 0/1:17,17:34:99:511,0,471
chr16   11802382        rs35377237      T       TG      613.73 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.102;DB;DP=43;ExcessHet=3.0103;FS=1.261;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=16.15;ReadPosRankSum=1.72;SOR=1.061;VQSLOD=1.06;culprit=ReadPosRankSum GT:AD:DP:GQ:PGT:PID:PL:PS       0|1:21,17:39:99:0|1:11802382_T_TG:651,0,831:11802382
chr16   11802387        rs35820990      G       T       661.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.87;DB;DP=43;ExcessHet=3.0103;FS=2.699;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=16.54;ReadPosRankSum=1.69;SOR=1.179;VQSLOD=1.71;culprit=ReadPosRankSum GT:AD:DP:GQ:PGT:PID:PL:PS       0|1:22,18:41:99:0|1:11802382_T_TG:690,0,848:11802382
chr16   11802389        rs35349341      G       T       661.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.51;DB;DP=43;ExcessHet=3.0103;FS=2.699;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=16.54;ReadPosRankSum=1.80;SOR=1.179;VQSLOD=1.67;culprit=ReadPosRankSum GT:AD:DP:GQ:PGT:PID:PL:PS       0|1:22,18:41:99:0|1:11802382_T_TG:690,0,848:11802382
chr16   11802625        rs7195390       T       C       425.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-3.395e+00;DB;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=13.73;ReadPosRankSum=2.31;SOR=0.910;VQSLOD=4.45;culprit=FS    GT:AD:DP:GQ:PL 0/1:12,19:31:99:454,0,376
chr18   11790984        rs772652795     TCC     T       894.73 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.855;DB;DP=50;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=18.26;ReadPosRankSum=-6.280e-01;SOR=0.784;VQSLOD=2.56;culprit=FS       GT:AD:DP:GQ:PL 0/1:25,24:49:99:932,0,968
chr18   11791216        rs1863121       G       A       1248.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=24.81;SOR=0.693;VQSLOD=5.14;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,32:32:96:1277,96,0
chr18   11791733        rs9303747       C       G       1218.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=31.25;SOR=1.911;VQSLOD=5.55;culprit=FS      GT:AD:DP:GQ:PL 1/1:0,32:32:96:1247,96,0
chr18   11792239        rs72867020      A       T       224.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.485;DB;DP=24;ExcessHet=3.0103;FS=1.685;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=9.77;ReadPosRankSum=-4.480e-01;SOR=1.230;VQSLOD=2.89;culprit=FS    GT:AD:DP:GQ:PL 0/1:15,8:24:99:253,0,522
chr18   11793111        rs10401123      G       C       353.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.549;DB;DP=41;ExcessHet=3.0103;FS=4.720;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=9.07;ReadPosRankSum=1.51;SOR=0.754;VQSLOD=1.29;culprit=QD GT:AD:DP:GQ:PL 0/1:25,14:39:99:382,0,741
chr18   11793324        rs10401100      T       C       424.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.492;DB;DP=37;ExcessHet=3.0103;FS=1.365;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=12.49;ReadPosRankSum=-1.220e-01;SOR=0.603;VQSLOD=4.15;culprit=ReadPosRankSum       GT:AD:DP:GQ:PL 0/1:19,15:34:99:453,0,528
chr18   11794528        rs4797579       A       G       304.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-3.668e+00;DB;DP=28;ExcessHet=3.0103;FS=6.239;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=12.19;ReadPosRankSum=0.00;SOR=1.492;VQSLOD=1.97;culprit=SOR   GT:AD:DP:GQ:PL 0/1:13,12:26:99:333,0,461
chr18   11795390        rs1339164174    CA      C       296.73 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.963;DB;DP=25;ExcessHet=3.0103;FS=7.402;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=14.84;ReadPosRankSum=1.27;SOR=2.001;VQSLOD=-5.690e-02;culprit=FS       GT:AD:DP:GQ:PL 0/1:7,13:23:99:334,0,187
chr18   11796575        rs760136358     C       CAAA    61.73   PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-7.810e-01;DB;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=5.14;ReadPosRankSum=-9.780e-01;SOR=0.905;VQSLOD=2.58;culprit=QD   GT:AD:DP:GQ:PGT:PID:PL:PS       0|1:9,3:14:99:0|1:11796575_C_CAAA:99,0,363:11796575
chr18   11796596        rs8098035       C       A       102.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.98;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=7.34;ReadPosRankSum=0.429;SOR=0.693;VQSLOD=2.92;culprit=QD      GT:AD:DP:GQ:PGT:PID:PL:PS       0|1:10,4:16:99:0|1:11796575_C_CAAA:131,0,392:11796575
chr18   11797030        rs9944802       T       C       231.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-1.940e+00;DB;DP=30;ExcessHet=3.0103;FS=8.923;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=8.28;ReadPosRankSum=-8.320e-01;SOR=1.706;VQSLOD=0.956;culprit=QD      GT:AD:DP:GQ:PL 0/1:18,10:29:99:260,0,589
chr18   11797740        rs143546710     CAGAG   C       530.73 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-6.270e-01;DB;DP=31;ExcessHet=3.0103;FS=1.518;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=18.95;ReadPosRankSum=-7.800e-02;SOR=1.032;VQSLOD=3.33;culprit=FS      GT:AD:DP:GQ:PL 0/1:13,15:28:99:568,0,480
chr18   11799183        rs9962277       C       T       501.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.649;DB;DP=25;ExcessHet=3.0103;FS=1.760;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=20.91;ReadPosRankSum=-1.777e+00;SOR=0.697;VQSLOD=2.32;culprit=FS   GT:AD:DP:GQ:PL 0/1:8,16:24:99:530,0,224
chr18   11800067        rs10468681      C       A       280.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.61;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.04;ReadPosRankSum=0.686;SOR=0.722;VQSLOD=5.54;culprit=FS GT:AD:DP:GQ:PL 0/1:11,9:20:99:309,0,381
chr18   11800408        rs9303748       C       T       682.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.861;DB;DP=42;ExcessHet=3.0103;FS=1.263;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=17.07;ReadPosRankSum=-6.600e-02;SOR=1.136;VQSLOD=4.16;culprit=FS   GT:AD:DP:GQ:PL 0/1:18,22:41:99:711,0,556
chr18   11800620        rs72867032      G       C       636.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-9.440e-01;DB;DP=46;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.15;ReadPosRankSum=-1.370e-01;SOR=0.807;VQSLOD=4.27;culprit=FS      GT:AD:DP:GQ:PL 0/1:24,21:45:99:665,0,786
chr18   11801730        rs34858453      GT      G       394.73 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.25;DB;DP=36;ExcessHet=3.0103;FS=3.174;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=10.96;ReadPosRankSum=0.185;SOR=1.445;VQSLOD=2.38;culprit=QD GT:AD:DP:GQ:PL 0/1:24,12:36:99:432,0,972
chr18   11802303        rs10048315      G       A       707.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-8.490e-01;DB;DP=53;ExcessHet=3.0103;FS=2.488;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=15.06;ReadPosRankSum=0.383;SOR=0.856;VQSLOD=1.64;culprit=FS   GT:AD:DP:GQ:PL 0/1:24,23:47:99:736,0,799
chr18   11802505        rs10048316      C       T       676.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.347;DB;DP=52;ExcessHet=3.0103;FS=2.373;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=13.27;ReadPosRankSum=0.904;SOR=1.059;VQSLOD=2.46;culprit=FS        GT:AD:DP:GQ:PL 0/1:29,22:51:99:705,0,948
chr18   11802992        rs9303749       C       T       444.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=4.58;DB;DP=39;ExcessHet=3.0103;FS=7.194;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=11.40;ReadPosRankSum=-1.430e+00;SOR=1.361;VQSLOD=2.19;culprit=ReadPosRankSum        GT:AD:DP:GQ:PL 0/1:24,15:39:99:473,0,497
chr18   11803083        rs9972997       T       C       605.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-1.501e+00;DB;DP=42;ExcessHet=3.0103;FS=2.694;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.42;ReadPosRankSum=1.03;SOR=0.825;VQSLOD=3.28;culprit=FS    GT:AD:DP:GQ:PL 0/1:21,21:42:99:634,0,667
chr19   11791513        rs12977679      A       G       590.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-1.250e+00;DB;DP=40;ExcessHet=3.0103;FS=2.636;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=15.15;ReadPosRankSum=-1.016e+00;SOR=0.561;VQSLOD=2.60;culprit=FS      GT:AD:DP:GQ:PL 0/1:19,20:40:99:619,0,607
chr19   11792756        rs10401430      A       G       86.77   PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.19;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=5.78;ReadPosRankSum=0.327;SOR=0.941;VQSLOD=3.61;culprit=QD GT:AD:DP:GQ:PL 0/1:11,4:15:99:115,0,310
chr19   11792786        rs12986106      C       A       80.77   PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.832;DB;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=6.21;ReadPosRankSum=-1.500e-01;SOR=1.329;VQSLOD=1.48;culprit=QD    GT:AD:DP:GQ:PL 0/1:9,4:13:99:109,0,273
chr19   11793268        rs371071500     CT      C       180.73 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.765;DB;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=20.08;ReadPosRankSum=0.00;SOR=0.859;VQSLOD=2.68;culprit=FS      GT:AD:DP:GQ:PL 0/1:2,7:9:43:218,0,43
chr19   11794128        rs425995        A       G       495.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-4.760e-01;DB;DP=34;ExcessHet=3.0103;FS=3.041;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.58;ReadPosRankSum=0.570;SOR=1.302;VQSLOD=3.55;culprit=ReadPosRankSum       GT:AD:DP:GQ:PL 0/1:18,16:34:99:524,0,627
chr19   11794274        rs286223        G       A       570.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.13;DB;DP=38;ExcessHet=3.0103;FS=1.273;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=15.43;ReadPosRankSum=0.532;SOR=0.446;VQSLOD=4.03;culprit=FS GT:AD:DP:GQ:PL 0/1:19,18:37:99:599,0,575
chr19   11794528        rs7253875       A       G       391.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-4.189e+00;DB;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=11.87;ReadPosRankSum=0.667;SOR=0.622;VQSLOD=5.62;culprit=FS   GT:AD:DP:GQ:PL 0/1:17,16:33:99:420,0,577
chr19   11795669        rs286225        C       T       48.77   PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.126;DB;DP=6;ExcessHet=3.0103;FS=3.979;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=9.75;ReadPosRankSum=0.126;SOR=0.859;VQSLOD=-8.980e-02;culprit=DP    GT:AD:DP:GQ:PL 0/1:2,3:5:35:77,0,35
chr19   11796087        rs286226        T       G       150.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-2.803e+00;DB;DP=16;ExcessHet=3.0103;FS=5.193;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=9.42;ReadPosRankSum=-1.540e-01;SOR=0.532;VQSLOD=1.09;culprit=QD       GT:AD:DP:GQ:PL 0/1:9,7:16:99:179,0,319
chr19   11796906        rs286228        C       T       432.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=4.07;DB;DP=23;ExcessHet=3.0103;FS=3.925;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=18.82;ReadPosRankSum=0.839;SOR=0.223;VQSLOD=2.67;culprit=QD GT:AD:DP:GQ:PL 0/1:10,13:23:99:461,0,209
chr19   11796977        rs286229        T       C       496.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-1.865e+00;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=20.70;ReadPosRankSum=-1.504e+00;SOR=0.741;VQSLOD=4.76;culprit=FS      GT:AD:DP:GQ:PL 0/1:8,16:24:99:525,0,247
chr19   11797055        rs286230        A       G       435.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-1.882e+00;DB;DP=27;ExcessHet=3.0103;FS=3.565;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=16.14;ReadPosRankSum=-9.960e-01;SOR=0.223;VQSLOD=3.41;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:13,14:27:99:464,0,433
chr19   11797089        rs286231        T       A       565.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.38;DB;DP=30;ExcessHet=3.0103;FS=8.869;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=19.51;ReadPosRankSum=-1.307e+00;SOR=0.718;VQSLOD=1.39;culprit=FS    GT:AD:DP:GQ:PL 0/1:12,17:29:99:594,0,348
chr19   11797582        rs286232        A       G       338.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-7.100e-02;DB;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=12.10;ReadPosRankSum=-2.462e+00;SOR=0.760;VQSLOD=5.15;culprit=FS      GT:AD:DP:GQ:PL 0/1:16,12:28:99:367,0,530
chr19   11797955        rs286233        A       G       612.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-2.349e+00;DB;DP=33;ExcessHet=3.0103;FS=1.523;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=19.77;ReadPosRankSum=-1.829e+00;SOR=0.738;VQSLOD=3.86;culprit=FS      GT:AD:DP:GQ:PL 0/1:9,22:31:99:641,0,264
chr19   11798192        rs5827137       TGCCTG T       454.73 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.53;DB;DP=38;ExcessHet=3.0103;FS=8.940;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.67;ReadPosRankSum=0.461;SOR=0.349;VQSLOD=2.35;culprit=FS GT:AD:DP:GQ:PL 0/1:18,13:31:99:492,0,716
chr19   11798757        rs286234        G       A       703.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=5.16;DB;DP=41;ExcessHet=3.0103;FS=15.322;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=17.17;ReadPosRankSum=0.365;SOR=1.317;VQSLOD=1.41;culprit=FS        GT:AD:DP:GQ:PL 0/1:20,21:41:99:732,0,535
chr19   11799463        rs184056        C       T       97.77   PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-1.173e+00;DB;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=6.98;ReadPosRankSum=0.065;SOR=0.631;VQSLOD=3.89;culprit=QD    GT:AD:DP:GQ:PL 0/1:9,5:14:99:126,0,299
chr19   11799502        rs34472985      C       CTT     69.73   PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.854;DB;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=8.72;ReadPosRankSum=0.439;SOR=0.307;VQSLOD=1.44;culprit=FS      GT:AD:DP:GQ:PL 0/1:5,3:8:99:107,0,188
chr19   11799664        rs286236        G       A       430.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.42;DB;DP=24;ExcessHet=3.0103;FS=3.963;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=18.73;ReadPosRankSum=-3.110e-01;SOR=0.442;VQSLOD=0.150;culprit=QD       GT:AD:DP:GQ:PL 0/1:10,13:23:99:459,0,280
chr19   11799679        rs286237        C       T       355.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-6.700e-02;DB;DP=22;ExcessHet=3.0103;FS=6.373;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=16.17;ReadPosRankSum=-2.640e-01;SOR=0.707;VQSLOD=1.37;culprit=ReadPosRankSum GT:AD:DP:GQ:PL 0/1:10,12:22:99:384,0,308
chr19   11800515        rs529515412     CTTTT   C,CTTTTT        857.73 PASS    AC=1,1;AF=0.500,0.500;AN=2;DB;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;QD=32.99;SOR=1.022;VQSLOD=5.63;culprit=FS        GT:AD:DP:GQ:PL     1/2:0,13,13:26:99:895,413,548,520,0,489
chr19   11800731        rs286238        A       T       675.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.475;DB;DP=41;ExcessHet=3.0103;FS=3.092;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=17.78;ReadPosRankSum=-7.420e-01;SOR=0.438;VQSLOD=1.98;culprit=ReadPosRankSum       GT:AD:DP:GQ:PL 0/1:16,22:38:99:704,0,491
chr19   11800812        rs7260645       T       C       551.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-8.080e-01;DB;DP=35;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=-8.600e-01;POSITIVE_TRAIN_SITE;QD=15.76;ReadPosRankSum=-4.970e-01;SOR=0.542;VQSLOD=5.09;culprit=FS        GT:AD:DP:GQ:PL 0/1:16,19:35:99:580,0,491
chr19   11801436        rs74180187      C       A       419.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.19;DB;DP=23;ExcessHet=3.0103;FS=1.744;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=18.25;ReadPosRankSum=-4.990e-01;SOR=0.283;VQSLOD=2.94;culprit=FS    GT:AD:DP:GQ:PGT:PID:PL:PS       0|1:10,13:23:99:0|1:11801436_C_A:448,0,297:11801436
chr19   11801438        rs4804172       T       C       828.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=32.51;SOR=1.179;VQSLOD=5.16;culprit=FS      GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:0,23:23:69:1|1:11801436_C_A:857,69,0:11801436
chr19   11801891        rs431393        A       G       349.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-1.831e+00;DB;DP=37;ExcessHet=3.0103;FS=2.870;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=9.72;ReadPosRankSum=-7.430e-01;SOR=0.574;VQSLOD=2.77;culprit=QD       GT:AD:DP:GQ:PL 0/1:22,14:37:99:378,0,745

agh for 1298 A>C (rs1801131) I need to grep "rs1801131" which returns no matches. So nebula's pre-provided vcf file does not work... nebula does provide BAM and FASTQ files but these are a bigger hassle and I may do other things before returning to this...

Edited October 5, 2023 by InquilineKea

Alex K Chen · October 5, 2023

trying to do MTHFR variant... I think the vcf file doesn't show some variants (why nebula chooses to include some is known only to #MacawGod), but some of these match up with known rs values...

2023-10-04_225337.png.e7560ba3938808bcba4e7a896ef63824.png

Edited October 5, 2023 by InquilineKea

Alex K Chen · October 5, 2023

Wow, if I want to find all my variants of the COMT gene, this is how to do it:

grep "^chr22" nebulafile.vcf | awk '$2 >= 19941772 && $2 <= 19969975' > filtered_variants.vcf\

...and there are A LOT...

===

for FOXO3 (JUST for the coding region - the uncoded region is larger -https://genome.ucsc.edu/cgi-bin/hgGene?hgsid=1722460280_ZpgnPPsHACkmsNEERu7KHYVoeSAh&hgg_section_mrnaDescriptions_close=1 ), it's

grep "^chr6" nebula.vcf | awk '$2 >= 108561209 && $2 <= 108664855' > filtered_variants.vcf

[nebula uses reference gene 38]...

[i just installed windows subsystem for linux today AT LAST]... and sublime text 4 to view large files...

.chr6 108587315 rs2802292 G T 1336.77 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.52;DB;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=32.26;ReadPosRankSum=1.73;SOR=0.269;VQSLOD=3.99;culprit=FS GT:AD:DP:GQ:PL 1/1:1,36:37:77:1365,77,0

Alternate allele here, not pro-longevity...

Quote

Only genetic variation within the FOXO3A gene was found to have a significant association with human longevity. The natural genetic variation within the FOXO3A gene (rs2802292; variable name: FOXO3A3) showed that the long-lived Japanese had one or more copies of the “G” allele of the FOXO3A gene. In contrast to the “G” allele in long-lived people, a higher “T” allele frequency of the FOXO3A gene was found in average-lived (about 77 years of age) Japanese men. The overall risk (OR) for TT homozygous minor genotype versus GG homozygous major genotype between the cases and controls was 2.75 (p = 0.0007) (Willcox et al., 2008). In addition, the authors tested the relationship between lifetime prevalence of several chronic diseases and FOXO3A genotype among 3741 men aged 71–93 years. The authors found that the GG homozygous carriers were healthier at baseline than GT heterozygous and TT homozygous carriers when comparing the health status of subjects with the definition of high physical function

FOXO3_variants.vcf

Edited October 5, 2023 by InquilineKea

Alex K Chen · October 5, 2023

SIRT6

Quote

grep "^chr19" alexchennebula.vcf | awk '$2 >= 4174109 && $2 <= 4182563'
chr19   4174401 rs350846        C       G       1066.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=31;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=34.41;SOR=0.756;VQSLOD=6.73;culprit=QD     GT:AD:DP:GQ:PL 1/1:0,31:31:92:1095,92,0
chr19   4174472 rs1159824959    G       A       516.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=3.51;DB;DP=24;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;QD=22.47;ReadPosRankSum=0.807;SOR=0.446;VQSLOD=3.45;culprit=FS GT:AD:DP:GQ:PL 0/1:8,15:23:99:545,0,162
chr19   4174953 rs350845        A       G       793.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=31.47;SOR=2.303;VQSLOD=1.78;culprit=FS        GT:AD:DP:GQ:PGT:PID:PL:PS        1|1:0,22:22:66:1|1:4174945_T_G:822,66,0:4174945
chr19   4176088 rs107251        T       C       1266.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.46;SOR=0.836;VQSLOD=6.48;culprit=FS     GT:AD:DP:GQ:PL 1/1:0,43:43:99:1295,129,0
chr19   4177054 rs350844        A       G       389.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=16;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=24.36;SOR=2.049;VQSLOD=4.09;culprit=FS     GT:AD:DP:GQ:PL 1/1:0,16:16:47:418,47,0
chr19   4177334 rs350843        A       C       840.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=27;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=33.63;SOR=1.358;VQSLOD=5.81;culprit=FS     GT:AD:DP:GQ:PL 1/1:0,25:25:74:869,74,0
chr19   4178265 rs141863180     T       C       156.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-2.709e+00;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=7.13;ReadPosRankSum=-7.050e-01;SOR=0.856;VQSLOD=4.38;culprit=QD   GT:AD:DP:GQ:PL 0/1:15,7:22:99:185,0,526
chr19   4179639 rs352492        C       T       192.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.80;DB;DP=20;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=10.15;ReadPosRankSum=0.507;SOR=1.085;VQSLOD=3.43;culprit=FS     GT:AD:DP:GQ:PL 0/1:12,7:19:99:221,0,345
chr19   4180693 rs7260071       T       G       556.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-1.123e+00;DB;DP=42;ExcessHet=3.0103;FS=12.871;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=13.92;ReadPosRankSum=-7.800e-02;SOR=2.518;VQSLOD=0.835;culprit=FS        GT:AD:DP:GQ:PL 0/1:21,19:41:99:585,0,697
chr19   4180839 rs352493        C       T       319.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.43;DB;DP=24;ExcessHet=3.0103;FS=10.942;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.53;ReadPosRankSum=-7.890e-01;SOR=2.442;VQSLOD=1.02;culprit=FS       GT:AD:DP:GQ:PL 0/1:11,11:22:99:348,0,287

Some of the rs names cluster together, since they came together as part of the same research paper... rs names with "lower" indices were discovered earlier, and probably have more written about them.

=======

interpret this: "chr19 4176088 rs107251 T C 1266.77 PASS AC=2;AF=1.00;AN=2;DB;DP=43;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.46;SOR=0.836;VQSLOD=6.48;culprit=FS GT:AD:DP:GQ:PL 1/1:0,43:43:99:1295,129,0"

ChatGPT

Quote

Certainly! This entry is from a VCF (Variant Call Format) file, which provides information about a genomic variant. Let's break it down step-by-step:

chr19: The chromosome on which the variant is located. Here, it's chromosome 19.

4176088: The position on chromosome 19 where the variant occurs.

rs107251: The identifier for the variant, typically an rsID from the dbSNP database. This helps in linking to external databases for more information about this variant.

T: The reference allele, which means this is the base present in the reference genome at this position.

C: The alternate allele, indicating the variant base observed in this sample.

1266.77: The quality score of the variant call. A higher score typically indicates a higher confidence in the variant call.

PASS: This suggests the variant has passed all filters applied during variant calling, indicating it's of good quality.

The INFO field contains several annotations:

AC=2: Alt allele count in genotype, indicating there are two copies of the alternate allele in the sample.

AF=1.00: Alt allele frequency. A frequency of 1.00 or 100% indicates that both alleles in the sample are the alternate allele.

AN=2: Total number of alleles in the called genotypes.

DB: Suggests this variant is recorded in the dbSNP database.

DP=43: Total read depth at this position, indicating that 43 sequencing reads overlapped this position.

ExcessHet=3.0103, FS=0.000, QD=29.46, SOR=0.836, and others: These are various metrics and annotations that provide insight into the variant's quality, its nature, and the confidence in the variant call. For instance, QD (Quality by Depth) is a normalized quality score, and SOR (Strand Odds Ratio) provides insight into potential strand bias.

POSITIVE_TRAIN_SITE: Indicates the variant was used as a "positive" example during the variant recalibration process.

culprit=FS: Points out the primary annotation that contributed most to the variant being assigned its recalibration score.

The sample-specific columns:

GT:AD:DP:GQ:PL: Describes the data format in the sample columns.

1/1:0,43:43:99:1295,129,0: The sample data. The genotype 1/1 suggests it's a homozygous alternate variant. 0,43 is the allele depth, showing 0 reads supporting the reference and 43 supporting the alternate allele. DP=43 is consistent with the sum of these depths. GQ=99 indicates a high confidence in the genotype call. The PL values are Phred-scaled likelihoods for various genotype states.

In summary, this entry describes a homozygous variant on chromosome 19 at position 4176088, where the reference allele T is replaced by the alternate allele C in the sample.

I am at least advantaged in this

Quote

rs107251

SNPedia
https://www.snpedia.com › index.php › Rs107251

Jan 10, 2021 — One study found that individuals with either the CC or CT genotype at rs107251 within SIRT6 displayed >5-year mean survival advantages ...

Edited October 5, 2023 by InquilineKea

Alex K Chen · October 5, 2023

TOMM40 sites [note the grep includes extra rs values...]:

Quote

grep -E "rs2075650|rs10524523|rs157582|rs71352238|rs8106922" alexchennebula.vcf
chr1    175799204       rs1575824       T       C       400.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=23.57;SOR=1.371;VQSLOD=3.23;culprit=FS
GT:AD:DP:GQ:PL 1/1:0,17:17:50:429,50,0
chr1    175799384       rs1575825       C       G       1085.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=34.70;SOR=1.609;VQSLOD=6.42;culprit=QD
GT:AD:DP:GQ:PL 1/1:0,30:31:90:1114,90,0
chr10   8608486 rs1575823       G       A       1008.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=26;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=27.09;SOR=1.981;VQSLOD=4.92;culprit=FS GT:AD:DP:GQ:PL 1/1:0,26:26:78:1037,78,0
chr19   44891079        rs71352238      T       C       565.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-3.600e-02;DB;DP=34;ExcessHet=3.0103;FS=3.211;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=16.64;ReadPosRankSum=-1.068e+00;SOR=0.260;VQSLOD=3.84;culprit=SOR     GT:AD:DP:GQ:PL 0/1:14,20:34:99:594,0,417
chr19   44892362        rs2075650       A       G       431.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-2.509e+00;DB;DP=27;ExcessHet=3.0103;FS=10.243;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=16.61;ReadPosRankSum=-3.900e-01;SOR=2.833;VQSLOD=1.00;culprit=FS     GT:AD:DP:GQ:PL 0/1:11,15:26:99:460,0,356
chr19   44892962        rs157582        C       T       481.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.330;DB;DP=35;ExcessHet=3.0103;FS=1.356;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.60;ReadPosRankSum=-1.622e+00;SOR=0.425;VQSLOD=4.41;culprit=FS   GT:AD:DP:GQ:PL 0/1:17,16:33:99:510,0,572
chrX    46045982        rs1575820       G       T       525.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=26.06;SOR=0.976;VQSLOD=4.47;culprit=FS
GT:AD:DP:GQ:PL 1/1:0,14:14:42:554,42,0
chrX    46050297        rs1575821       G       T       417.77 PASS    AC=2;AF=1.00;AN=2;BaseQRankSum=1.64;DB;DP=14;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=29.84;ReadPosRankSum=1.24;SOR=0.446;VQSLOD=2.68;culprit=FS    GT:AD:DP:GQ:PL 1/1:1,13:14:32:446,32,0

I am hetereozygeous at all 3 sites for TOMM40...

Edited October 5, 2023 by InquilineKea

Alex K Chen · October 5, 2023

This is mostly *not* good, and is the opposite of my OakVar report... (I did send in my OakVar report to someone, maybe the software is still buggy). [the OakVar report *was* bugged, b/c it lists ref and alt alleles as the same... this is why my PRS score is not optimal.......)

Quote

inquilinekea@User-PC:~/link_to_current_dir/Downloads$ grep -w "rs9400239" alexchennebula.vcf
chr6    108656460       rs9400239       T       C       1518.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=28.75;SOR=0.954;VQSLOD=6.91;culprit=FS
GT:AD:DP:GQ:PL 1/1:0,40:41:99:1547,120,0
inquilinekea@User-PC:~/link_to_current_dir/Downloads$ grep -w "rs2764264" alexchennebula.vcf
chr6    108613258       rs2764264       C       T       1049.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=28;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=32.86;SOR=1.101;VQSLOD=6.99;culprit=FS
GT:AD:DP:GQ:PL 1/1:0,27:27:81:1078,81,0
inquilinekea@User-PC:~/link_to_current_dir/Downloads$ grep -w "rs2802292" alexchennebula.vcf
chr6    108587315       rs2802292       G       T       1336.77 PASS    AC=2;AF=1.00;AN=2;BaseQRankSum=1.52;DB;DP=37;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=32.26;ReadPosRankSum=1.73;SOR=0.269;VQSLOD=3.99;culprit=FS    GT:AD:DP:GQ:PL 1/1:1,36:37:77:1365,77,0
inquilinekea@User-PC:~/link_to_current_dir/Downloads$ grep -w "rs13217795" alexchennebula.vcf
chr6    108652895       rs13217795      C       T       1473.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=42;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.83;SOR=0.693;VQSLOD=6.52;culprit=FS
GT:AD:DP:GQ:PL 1/1:0,40:40:99:1502,119,0
inquilinekea@User-PC:~/link_to_current_dir/Downloads$ grep -w "rs2802288" alexchennebula.vcf
chr6    108575012       rs2802288       A       G       982.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=31.70;SOR=0.892;VQSLOD=7.43;culprit=FS
GT:AD:DP:GQ:PL 1/1:0,31:31:93:1011,93,0
inquilinekea@User-PC:~/link_to_current_dir/Downloads$ grep -w "rs2802290" alexchennebula.vcf
chr6    108584477       rs2802290       G       A       1485.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=31.93;SOR=0.850;VQSLOD=6.99;culprit=FS
GT:AD:DP:GQ:PL 1/1:0,39:39:99:1514,117,0
inquilinekea@User-PC:~/link_to_current_dir/Downloads$

Quoted from the geneticfuture article: "No-one should consider this association to be definitive until it's been replicated in independent cohorts. Secondly, the effects of this variant are likely to differ between groups. According to the HapMap database the frequency of the "die early" (T) version of the variant varies substantially between populations: it's around 76% in Japanese, slightly more common (81%) in Chinese, less common (58%) in Europeans, and quite rare (17%) in West Africans. Given that the Japanese have the highest life expectancy of any of these populations, this is a counter-intuitive result, which reinforces the fact that there are many genes and other factors influencing variation in longevity."

Ugh, the Romanians (Anton Kulaga) did find my longevity PRS to be... 9%. Knowing my blood test results and family, this goes against all intuition, but due to small effect sizes (or rarity) of longevity-promoting SNPs, all the individual genetic variants of longevity still explain only a very small fraction of extreme longevity... It sucks that I suck at the FOXO3 loci though there are many factors upstream of FOXO3 expression and only a proteomic/metabolomics blood test can really figure out what is happening at FOXO3 (and even then it's not the whole story because you have receptors...)

Even if you don't die from any of the *standard diseases*, you can still end up like Jimmy Carter and make it to 99 while very severely frail... (b/c Jimmy Carter is still not a slow ager, despite him not *degenerating from the standard diseases that typically kill people*)... Mahathir Mohamad is a very slow ager who has more standard cardiac risk factors that can kill people...

...If I suck at FOXO3, there's always gene therapy in 5-10 years...

Quote

grep rs4946936 alexchennebula.vcf
chr6 108682118 rs4946936 T C 1527.77 PASS AC=2;AF=1.00;AN=2;DB;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=28.85;SOR=1.292;VQSLOD=6.67;culprit=FS
GT:AD:DP:GQ:PL 1/1:0,40:40:99:1556,120,0

this is slightly good

Edited October 5, 2023 by InquilineKea

Alex K Chen · October 5, 2023

I can't find https://www.snpedia.com/index.php/Rs12212067

Alex K Chen · October 5, 2023

Trying to match up with supp table 1 of https://academic.oup.com/biomedgerontology/article/76/5/750/5996044#supplementary-data

[REMOVE EMPTY LINES for grep not to output everything]. there are so many variants starting with rs6224

"bad homo" variants are in red. hetereo in purple. "good homo" in green.

Table S2: Genetic variants previoously associated with longevity in GWAS studies
Chr	Position	Rsid	A1	Freq	Gene	Study
1	109821797	rs4970836	G	0.23	CELSR2/PSRC1	Timmers et al. (2019)
1	114173410	rs1230666	G	0.85	MAGI3	Timmers et al. (2019)
2	628524	rs6744653	A	0.17	TMEM18	Timmers et al. (2019)
2	26932887	rs1275922	G	0.74	KCNK3	Timmers et al. (2019)
2	237081854	rs10211471	C	0.80	GBX2/ASB18	Timmers et al. (2019)
4	8565547	rs7676745	G	0.96	GPR78/CPZ	Deelen et al. (2019)
6	31147476	rs3130507	G	0.75	POU5F1/TCF19	Timmers et al. (2019)
6	32591248	rs34967069	T	0.07	HLA-DRB5/HLA-DQA1	Timmers et al. (2019)
6	108998266	rs3800231	A	0.29	FOXO3	Broer et al. (2015)
6	161010118	rs10455872	A	0.92	LPA	Timmers et al. (2019)
7	6189780	rs3764814	C	0.17	USP42	Sebastiani et al. (2017)
7	22768027	rs2069837	A	0.07	IL6	Zeng et al. (2016)
7	75094329	rs113160991	G	0.78	POM121C/STAG3L1/SPDYE5	Timmers et al. (2019)
7	129685597	rs56179563	A	0.39	ZC3HC1/KLHDC10	Timmers et al. (2019)
9	22098619	rs1556516	G	0.50	CDKN2B/CDKN2A	Timmers et al. (2019)
9	136141870	rs2519093	C	0.81	ABO	Timmers et al. (2019)
11	233212	rs11555236	A	0.19	SIRT3	Albani et al. (2014)
11	113639842	rs61905747	A	0.81	ZW10/CLDN25	Timmers et al. (2019)
12	83438559	rs7976168	A	0.32	TMTC2	Sebastiani et al. (2017)
12	112059557	rs11065979	C	0.56	ATXN2/BRAP	Timmers et al. (2019)
13	19440123	rs2440012	C	0.76	-	Zeng et al. (2016)
13	64836488	rs61949650	C	0.07	-	Timmers et al. (2019)
15	78817929	rs8042849	T	0.65	HYKK/PSMA4	Timmers et al. (2019)
15	91423543	rs6224	G	0.52	FURIN/FES	Timmers et al. (2019)
15	99478225	rs2229765	A	0.40	IGF1R	Albani et al. (2011)
16	72075593	rs12924886	A	0.80	HP/DHODH	Timmers et al. (2019)
19	11190534	rs142158911	A	0.12	LDLR/SMARCA4	Timmers et al. (2019)
19	45411941	rs429358	T	0.85	APOE	Timmers et al. (2019)
19	45412079	rs7412	T	0.09	APOE	Deelen et al. (2019)
Chr: chromosome; Position: genomic position according to GRCh37 (hg19); Rsid: variant identifier; A1: longevity-associated allele; Freq A1: frequency of longevity-associated allele; Gene: gene(s) associated with the variant in the original study; Study: study from which the association was found, together with year of publication. Reference to the original studies are:15,16,19–21,63,64

Quote

grep -Fwf rs_list.txt alexchennebula.vcf
chr1    109279175       rs4970836       G       A       199.84 PASS    AC=2;AF=1.00;AN=2;DB;DP=6;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=33.31;SOR=1.329;VQSLOD=3.78;culprit=FS
GT:AD:DP:GQ:PL 1/1:0,6:6:18:228,18,0
chr1    113630788       rs1230666       A       G       1545.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=32.80;SOR=1.075;VQSLOD=7.42;culprit=FS
GT:AD:DP:GQ:PL 1/1:0,41:41:99:1574,123,0
chr2    628524 rs6744653       A       G       1166.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=38;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=30.70;SOR=0.798;VQSLOD=7.60;culprit=FS GT:AD:DP:GQ:PL 1/1:0,38:38:99:1195,114,0
chr2    26710019        rs1275922       A       G       651.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=23;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=29.63;SOR=0.874;VQSLOD=5.72;culprit=FS
GT:AD:DP:GQ:PL 1/1:0,22:22:66:680,66,0
chr2    236173211       rs10211471      C       T       245.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.22;DB;DP=22;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=11.17;ReadPosRankSum=-3.300e-02;SOR=0.693;VQSLOD=5.01;culprit=FS    GT:AD:DP:GQ:PL 0/1:12,10:22:99:274,0,242
chr6    31179699        rs3130507       G       A       483.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.84;DB;DP=33;ExcessHet=3.0103;FS=3.093;MLEAC=1;MLEAF=0.500;MQRankSum=-9.100e-01;POSITIVE_TRAIN_SITE;QD=15.61;ReadPosRankSum=-7.210e-01;SOR=0.494;VQSLOD=3.45;culprit=ReadPosRankSum GT:AD:DP:GQ:PGT:PID:PL:PS      0|1:16,15:33:99:1|0:31179698_C_T:512,0,627:31179698
chr6    108677063       rs3800231       A       G       1114.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=34.84;SOR=1.112;VQSLOD=6.59;culprit=QD
GT:AD:DP:GQ:PL 1/1:0,32:32:96:1143,96,0
chr7    6150149 rs3764814       T       C       1133.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=32;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=28.70;SOR=0.693;VQSLOD=6.92;culprit=FS GT:AD:DP:GQ:PL 1/1:0,30:30:90:1162,90,0
chr7    75465064        rs113160991     A       G       488.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;QD=25.72;SOR=0.793;VQSLOD=3.59;culprit=FS      GT:AD:DP:GQ:PL
1/1:0,19:19:56:517,56,0
chr7    130045757       rs56179563      G       A       229.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=1.04;DB;DP=27;ExcessHet=3.0103;FS=4.039;MLEAC=1;MLEAF=0.500;MQRankSum=-1.090e+00;POSITIVE_TRAIN_SITE;QD=9.57;ReadPosRankSum=-5.970e-01;SOR=1.863;VQSLOD=1.51;culprit=QD       GT:AD:DP:GQ:PL 0/1:15,9:26:99:258,0,481
chr9    22100177        rs1556516       G       C       936.77 PASS    AC=2;AF=1.00;AN=2;BaseQRankSum=1.76;DB;DP=29;ExcessHet=3.0103;FS=4.929;MLEAC=2;MLEAF=1.00;MQRankSum=0.00;NEGATIVE_TRAIN_SITE;POSITIVE_TRAIN_SITE;QD=34.70;ReadPosRankSum=0.496;SOR=1.646;VQSLOD=0.973;culprit=QD      GT:AD:DP:GQ:PL 1/1:1,26:28:71:965,71,0
chr12   83044780        rs7976168       A       G       398.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-2.583e+00;DB;DP=31;ExcessHet=3.0103;FS=3.352;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.24;ReadPosRankSum=-1.310e+00;SOR=0.260;VQSLOD=4.00;culprit=SOR     GT:AD:DP:GQ:PL 0/1:15,13:29:99:427,0,530
chr13   18865983        rs2440012       C       G       229.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=0.923;DB;DP=30;ExcessHet=3.0103;FS=1.661;MLEAC=1;MLEAF=0.500;MQRankSum=-1.109e+00;POSITIVE_TRAIN_SITE;QD=7.92;ReadPosRankSum=-1.123e+00;SOR=1.085;VQSLOD=2.34;culprit=QD      GT:AD:DP:GQ:PL 0/1:20,9:30:99:258,0,657
chr15   78525587        rs8042849       C       T       1236.77 PASS    AC=2;AF=1.00;AN=2;DB;DP=33;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=28.29;SOR=1.473;VQSLOD=5.65;culprit=FS
GT:AD:DP:GQ:PL 1/1:0,32:32:96:1265,96,0
chr15   98934996        rs2229765       G       A       447.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=2.29;DB;DP=38;ExcessHet=3.0103;FS=2.944;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=12.10;ReadPosRankSum=0.696;SOR=1.014;VQSLOD=3.93;culprit=ReadPosRankSum     GT:AD:DP:GQ:PL 0/1:22,15:37:99:476,0,721
chr16   72041694        rs12924886      A       T       233.77 PASS    AC=1;AF=0.500;AN=2;BaseQRankSum=-5.670e-01;DB;DP=27;ExcessHet=3.0103;FS=3.722;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=8.66;ReadPosRankSum=-1.231e+00;SOR=1.571;VQSLOD=1.62;culprit=QD       GT:AD:DP:GQ:PL 0/1:17,10:27:99:262,0,599

chr6 124576550 rs497756 A T 590.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.526;DB;DP=38;ExcessHet=3.0103;FS=1.281;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=15.55;ReadPosRankSum=1.01;SOR=0.392;VQSLOD=4.49;culprit=FS GT:AD:DP:GQ:PL 0/1:20,18:38:99:619,0,668

Edited October 5, 2023 by InquilineKea

Alex K Chen · October 5, 2023

https://www.ebi.ac.uk/gwas/variants/rs1556516

appears bad esp b/c it seems to be 50/50 in the population and I have the risk allele... Also CDKN2B seems important. Ugh.

If the "good" allele is at low frequency (eg for some of the FOXO3 variants), it doesn't change *that* much if you don't have it. If the "good" allele is at 50/50 frequency, it hurts. Most of my "red" is just for "low frequency good alleles" so this mostly does not seem to change much.

If the "good" allele is at very high frequency (or the contrapositive - the "bad" allele is at very low frequency), then having the "bad" allele is *really bad*. I seem free of bad alleles (and I know I'm free from the really bad ones).

Most of this is not super-actionable, but it's an update in the direction that I don't have the genes for extreme longevity. I (and others) still have the intuition that something *really weird* is going on in my body (even for an Asian) and we all suspect it's due to genetic factors, but I still don't know *what* is causing the weirdness. I know I do well on PhenoAge (and somewhat well on GrimAge), but this can't highlight anything super-mechanistic. I can't CR. I just eat insane quantities of fruits/nuts/vegetables.

My parents aren't unhealthy, even though they eat a trashy diet (though not the worst). Otoh they aren't superagers.

If I keep TGF-beta/inflammation super-low, then maybe https://en.wikipedia.org/wiki/CDKN2B is less of an issue

Finally, the real variants are the extremely low frequency variants, of which everyone has many, so there is no excluding this.

Quote

missing heritability of many human traits, including common variants (here denoted by minor allele frequency [MAF] >5%) of very weak effect, low-frequency (MAF 1–5%) and rare variants (MAF <1%) of small to modest effect, or a combination of both, with several possible scenarios all deemed plausible in simulation studies

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1212-4

Edited October 5, 2023 by InquilineKea

Alex K Chen · October 5, 2023

D6D is important too (for determing MUFA response), but I'm tired and I already know I don't get fat from MUFAs... it's not the most important gene..

Alex K Chen · October 5, 2023

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190315/

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029848

has ideas and doesn't implicate FOXO3

Here's the Joris Deelen paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6694136/ (it has SOME to say on FOXO3)...

Edited October 5, 2023 by InquilineKea

Alex K Chen · October 5, 2023

Quote

Tissue-specific genetically predicted expression of 14 genes (ANKRD31, BLOC1S1, KANSL1, CRHR1, ARL17A, LRRC37A2, ERCC1, RELB, DMPK, CD3EAP, PVRL2, GEMIN7, BLOC1S3, and APOC2) was significantly associated with survival to the 90th and/or 99th percentile age after adjustment for multiple testing (Table 5). Eight of these genes (ERCC1, RELB, DMPK, CD3EAP, PVRL2, GEMIN7, BLOC1S3, and APOC2) are located near the APOE gene, raising the likely possibility that these associations reflected the influence of variants in this well-established longevity-associated

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6694136/

EAF is effect allele frequency.

EA effect allele, OA other allele, EAF effect allele frequency, OR odds ratio (i.e., odds to become long-lived when carrying the effect allele []); 95% CI 95% confidence interval, I² heterogeneity statistic, P_het P-value for heterogeneity

Table 4

Results of the trans-ethnic genome-wide association meta-analyses

rsID	Chr:Position	Candidate/ closest gene	Alleles (EA/OA)	EAF	OR	95% CI	P	I² (%)	P _het
90th percentile cases versus all controls
rs12143832	1:21,705,436	ECE1	C/T	0.46	0.90	0.87–0.94	2.0 × 10⁻⁷	0	0.722
rs7676745	4:8,565,547	GPR78	A/G	0.04	0.67	0.58–0.78	1.7 × 10⁻⁷	1.8	0.428
rs1262476	6:126,986,996	−	A/G	0.24	1.12	1.07–1.17	9.8 × 10⁻⁷	0	0.574
rs2069837	7:22,768,027	IL6	G/A	0.08	0.90	0.82–0.99	5.2 × 10⁻⁸	50.7	0.005
rs35262860	8:55,478,909	RP1	GCT/G	0.39	1.11	1.07–1.15	5.6 × 10⁻⁷	0	0.955
rs62127362	19:33,458,479	CEP89	C/G	0.13	0.87	0.82–0.93	4.3 × 10⁻⁷	21.4	0.190
rs429358	19:45,411,941	APOE	C/T	0.13	0.60	0.55–0.66	1.0 × 10⁻⁶¹	52.1	0.004
rs7412	19:45,412,079	APOE	T/C	0.09	1.26	1.19–1.35	1.7 × 10⁻¹²	0	0.718
99th percentile cases versus all controls
rs2758603	1:156,198,994	PMF1	C/T	0.34	1.12	1.02–1.22	9.8 × 10⁻⁷	57.2	0.005
rs3830412	3:124,397,321	KALRN	A/AT	0.22	1.21	1.12–1.30	8.2 × 10⁻⁷	0	0.767
rs138762279	5:173,710,197	−	AT/A	0.16	0.79	0.72–0.86	2.2 × 10⁻⁷	0	0.769
rs2069837	7:22,768,027	IL6	G/A	0.09	0.90	0.76–1.08	1.4 × 10⁻⁸	67.7	3.5 × 10⁻⁴
rs7039467	9:22,056,213	CDKN2A/B	A/G	0.48	1.20	1.12–1.28	2.1 × 10⁻⁷	0	0.843
rs429358	19:45,411,941	APOE	C/T	0.13	0.55	0.50–0.61	1.3 × 10⁻³⁶	20.0	0.247
rs7412	19:45,412,079	APOE	T/C	0.09	1.39	1.26–1.53	1.7 × 10⁻¹²	10.0	0.347

Edited October 5, 2023 by InquilineKea

Alex K Chen · October 5, 2023

chr1 156229203 rs2758603 T C 249.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-2.153e+00;DB;DP=30;ExcessHet=3.0103;FS=3.581;MLEAC=1;MLEAF=0.500;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=8.61;ReadPosRankSum=-6.200e-01;SOR=0.193;VQSLOD=3.47;culprit=QD GT:AD:DP:GQ:PL 0/1:17,12:29:99:278,0,566

chr9 22056214 rs7039467 A G 329.77 PASS AC=2;AF=1.00;AN=2;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;POSITIVE_TRAIN_SITE;QD=32.98;SOR=0.693;VQSLOD=4.44;culprit=FS
GT:AD:DP:GQ:PL 1/1:0,10:10:30:358,30,0

I suck AGAIN on CDKN2A...

Edited October 5, 2023 by InquilineKea

Alex K Chen · October 5, 2023

Another set from BU centenarian study (I am too tired now)

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029848#pone.0029848.s022

Quote

137 SNPs of the 281 SNPs occur in 130 genes, some of which have been previously associated with aging such as LMNA (rs915179), WRN (rs1800392), and SOD2 (rs2758331) and several of them are in close proximity of coding SNPs [45]. The LMNA gene, which encodes the nuclear envelope proteins lamin A and lamin C, has been associated with the progeroid (premature aging-like) syndrome, Hutchinson-Gilford syndrome [46]. The WRN gene is a DNA helicase and exonuclease that plays a deterministic role in DNA repair and another progeroid syndrome, Werner's Syndrome [47]. The WRN gene has been associated with longevity in the Framingham Heart Study (FHS) sample [48]. It is remarkable that the two genes responsible for the best known progeroid syndromes appear in the genetic risk model, and this may reflect the power of the discovery sample which includes such extreme old ages. Another gene, also noted to be associated with longevity in the FHS sample as well as the Jerusalem Study, is SOD2, or superoxide dismutase 2 [49]. SOD2 is a key free radical scavenger and free radical damage likely plays an important pathogenic role in aging and numerous age-related diseases [50]. CDKN2A (rs1063192) performs a key step in the p53 pathway that has been posited to play a key role in inducing cellular senescence [51] and it has been associated with adult onset diabetes [52]. SORCS1 (rs7907713) and SORCS2 (rs6812745) have been linked AD [53]. Gastric inhibitory polypeptide (GIP), commonly referred to as glucose-dependent insulinotropic peptide, encodes a protein that regulates insulin secretion and activates AKT [54]. The association of this gene (rs9899404) supports the potential role of insulin regulation in exceptional longevity [55], and suggests new target genes for human aging beyond FOXO1, FOXO3A and IGF-IR [56], [57], [58]. There is also growing evidence of GIP playing a protective role in both diabetes and AD and GIP is being investigated as a therapeutic target [59].

The rate at which AI is progressing (short AI timelines) seems to come at the same rate (making up for it) that I'm not hearing *everything I want to hear* (though I still have no definitive proof of anything at the cellular level). I may QEEG again next week and this may also tell me things I don't want to hear...

Matt Kaeberlein just tweeted out that many "LEV people" are just "wishful thinking" (this IS inclusive of the AGI=>LEV crowd), but rapid progress in AGI *is* so weird that it has done way more to further distribute the LEV probability over ~50% (all bets are on the table) than anything.

For proteomics/metabolomics I'm thinking

Quote

Best bet is an academic center:1. Duke University School of Medicine offers LC-MS/MS differential expression analysis for $459 per sample for non-Duke scientists[1].
2. The University of Connecticut Proteomics & Metabolomics Facility offers various proteomics and metabolomics services with prices ranging from $35 to $500 per sample for external academic users[5].
3. The Roy J. Carver Biotechnology Center at the University of Illinois offers LC-MS/MS analysis with prices starting at $180 per sample for external academic users[2].
4. The Nebraska Center for Biotechnology offers targeted metabolomics services with prices starting at $115 per hour for external academic users[7].Please note that these prices may vary depending on the specific services required and the institution providing the service. It is recommended to contact the facilities directly for the most accurate pricing information and to discuss your specific needs.Citations:
[1] https://medschool.duke.edu/research/research-support/service-centers/core-research-facilities/proteomics-and-metabolomics-1
[2] https://biotech.illinois.edu/proteomics/pricing
[3] https://www.uthsc.edu/research/institutional-cores/pmc/services-and-fees.php
[4] https://core.uconn.edu/resource/proteomics/
[5] https://proteomics.uconn.edu/facility-rates/
[6] https://www.ccic.ohio-state.edu/MSP-Rates
[7] https://www.biotech.cornell.edu/core-facilities-brc/price-list/30
[8] https://biotech.unl.edu/proteomics-and-metabolomics

Edited October 5, 2023 by InquilineKea

Alex K Chen · October 5, 2023

https://elifesciences.org/articles/57849

https://elifesciences.org/for-the-press/53c636fb/do-people-aged-105-and-over-live-longer-because-they-have-more-efficient-dna-repair

Quote

They identified five common genetic changes that were more frequent in the 105+/110+ age groups, between two genes called COA1 and STK17A. When they cross-checked this against the published data, they found the same variants in the people aged over 100. Data acquired from computational analyses predicted that this genetic variability likely modulates the expression of three different genes.

The most frequently seen genetic changes were linked to increased activity of the STK17A gene in some tissues. This gene is involved in three areas important to the health of cells: coordinating the cell’s response to DNA damage, encouraging damaged cells to undergo programmed cell death and managing the amount of dangerous reactive oxygen species within a cell. These are important processes involved in the initiation and growth of many diseases such as cancer.

The most frequent genetic changes are also linked to reduced activity of the COA1 gene in some tissues. This gene is known to be important for the proper crosstalk between the cell nucleus and mitochondria – the energy-production factories in our cells whose dysfunction is a key factor in aging.

Additionally, the same region of the genome is linked to an increased expression of BLVRA in some tissues – a gene that is important to the health of cells due to its role in eliminating dangerous reactive oxygen species.

Alex K Chen · October 5, 2023

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9820206/

Quote

We discovered a suggestively significant (although not genome-wide significant) locus on chromosome 8 (rs9657521) that was associated with EL and which has not previously been reported in the literature. This locus is in a region of 8p23.1, which contains the genes GATA4, NEIL2, FDFT1, CTSB, and DEFB136. The protein signature that we found to be associated with rs9657521 includes PCSK1N, also known as proSAAS, IL18BP, SLAMF6, and CNTFR. The longevity-promoting allele of rs9657521 was associated with lower levels of the serum protein PCSK1N (see Figure

Ron Put · October 7, 2023

I'd take much of these a a large grain of salt. I took my first broad genetic test back in 2011 and have taken a couple of more since, including Nebula's 30x version.

If I were to take seriously each new study that claims to identify longevity genes or disease genes, I would be constantly either depressed or elated. I have x3.2 greater chance to live to 100, but 2x lower chance to live to 100. I am predisposed to high cholesterol, but also to lower cholesterol. I am predisposed to Alzheimer's disease but also have a lower chance of dementia...

There are some singe-gene diseases for which all this can be helpful, but most conditions are far, far more complex, and depend on too many genetic and lifestyle factors for current technology to be able to provide meaningful insights. I see it mostly as entertainment.

corybroo · October 8, 2023

Reinforcing Ron’s point, this article talks about a specific gene but many of our genes are similarly modulated by other genes as well as the environment. Usually we find a gene that protects or promotes some condition and then by examining the exceptions find other genes that affect (and possibly eliminate) the output of the first gene.

Kidney disease gene found to also have a protective mutation

increased risk of kidney disease due to a dangerous genetic mutation that creates a hole in the kidney cells, but Vanderbilt University Medical Center (VUMC) researchers have now discovered a protective genetic mutation that covers the hole to eliminate the risk.

immediate and broad implications for kidney health because people with both the disease-causing and protective mutation are not at increased risk.

Alex K Chen · June 2

In KL-VS, there are 2 nucleotide changes and they translate into different amino acids in 2 places of the klotho protein
- They speculate based on in vitro studies that Arking did in 2002, that in the klotho heterozygotes in which one allele is making a mutant protein, we think that there’s an overcompensation for that mutant protein by increasing wild type levels
  - Because what that variant does is it mucks up klotho secretion from the cell
- Just to be clear, carrying one variant is likely changing the structure and function of klotho, but there’s probably an overcompensation from the wild type allele causing higher levels of the wild type klotho
Peter would not have guessed that
He can’t believe he didn’t think to ask such an obvious question: Do the KL-VS individuals produce the same protein?

Alex K Chen · October 15

Quote

Just-DNA-SeqJust-DNA-Seq122 followers122 followers 2d • 2 days ago

Following

Is Metformin the Key to Longevity? Not for Everyone—Your Genes Might Decide!

💊 Metformin, widely known for its role in managing type 2 diabetes, is gaining attention as a potential geroprotector—a drug that could extend healthy lifespan by improving metabolic health and mitigating age-related diseases. Research has shown that metformin may reduce inflammation and mimic the effects of calorie restriction, positioning it as a promising candidate in longevity studies.

However, not all individuals respond equally to metformin. Recent research highlights that genetics 🧬 could be one of the critical factors determining this variability. For example, a study revealed that copy number loss in the PPARGC1A gene—a key regulator of mitochondrial biogenesis—was observed in non-responders to metformin treatment.
https://lnkd.in/eFrAnVi6
This discovery suggests that genomic differences might impact how well metformin can exert its beneficial effects on metabolism and longevity.

🟢 We are developing a new module for our platform, so everyone can check own genes, associated with metformin response

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What are the most important genome/SNP/SNPedia sites to query from a VCF file of one's genome? How do I visualize my genomic data

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EAF is effect allele frequency.

Table 4

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