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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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How to handle with missing field? #74

Closed liserjrqlxue closed 3 years ago

liserjrqlxue commented 3 years ago

In #63 we got how to ignore missing field with ('field name' in INFO). I think this ignore means skip or filter out. I want to treat missing field pass and go to check other rules. For example, I want to find high AF varant that meet --info "INFO.AF_popmax>0.9" but got missing field errors for some varants. I hope --info "INFO.AF_popmax>0.9 || INFO.AF>0.9" can get what I wanted, but wonder if varants missing AF_popmax will be filter by INFO.AF>0.9 or always keep/filter since the missing field error occur.

brentp commented 3 years ago

If I understand correctly, you can use:

--info '("AF_popmax" in INFO && INFO.AF_popmax > 0.9) || INFO>AF > 0.9'
liserjrqlxue commented 3 years ago

since there are variants with AC=0 missing AF field, I finally wrote a js function script below:

var config={
    AF_threshold:0.9,
}

function highAF(INFO){
    if (INFO.AC==0) {
        return false;
    }
    if (("AF_popmax" in INFO) && INFO.AF_popmax >= config.AF_threshold) {
        return true;
    }
    if (("AF" in INFO) && INFO.AF >= config.AF_threshold) {
        return true;
    }
    if (("AF_eas" in INFO) && INFO.AF_eas >= config.AF_threshold) {
        return true;
    }
    return false;
}

But when I check the filter result, I found variants below which should be filtered out and some may go wrong. Can you help to check if my js script may be wrong?

1   1292016 rs371756291 GCTGA   G   1869.88 RF  AC=1;AN=33082;AF=3.02279e-05;rf_tp_probability=0.195742;FS=150.725;InbreedingCoeff=0.0474;MQ=58.11;MQRankSum=0.358;QD=3.06;ReadPosRankSum=0.572;SOR=1.387;BaseQRankSum=-1.231;ClippingRankSum=0.286;DP=1410027;VQSLOD=-21.58;VQSR_culprit=FS;rf_negative_label;rf_label=FP;rf_train;variant_type=mixed;allele_type=del;n_alt_alleles=2;was_mixed;pab_max=1;gq_hist_alt_bin_freq=0|0|0|0|1|1|0|2|1|0|0|0|0|1|0|0|0|0|0|4;gq_hist_all_bin_freq=15639|33370|14682|21957|12712|3848|4306|1931|494|611|282|103|202|55|111|38|116|15|99|5645;dp_hist_alt_bin_freq=3|2|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|1|0;dp_hist_alt_n_larger=3;dp_hist_all_bin_freq=67441|41320|8973|1456|392|248|197|219|260|340|379|457|444|472|426|410|356|300|300|301;dp_hist_all_n_larger=1057;ab_hist_alt_bin_freq=0|1|2|3|1|1|2|0|0|0|0|0|0|0|0|0|0|0|0|0;AC_nfe_seu=0;AN_nfe_seu=602;AF_nfe_seu=0;nhomalt_nfe_seu=0;controls_AC_afr_male=0;controls_AN_afr_male=356;controls_AF_afr_male=0;controls_nhomalt_afr_male=0;non_neuro_AC_eas_kor=0;non_neuro_AN_eas_kor=436;non_neuro_AF_eas_kor=0;non_neuro_nhomalt_eas_kor=0;non_topmed_AC_amr=0;non_topmed_AN_amr=4634;non_topmed_AF_amr=0;non_topmed_nhomalt_amr=0;non_cancer_AC_asj_female=0;non_cancer_AN_asj_female=376;non_cancer_AF_asj_female=0;non_cancer_nhomalt_asj_female=0;AC_raw=10;AN_raw=232432;AF_raw=4.30233e-05;nhomalt_raw=0;AC_fin_female=0;AN_fin_female=5780;AF_fin_female=0;nhomalt_fin_female=0;non_cancer_AC_oth_female=0;non_cancer_AN_oth_female=304;non_cancer_AF_oth_female=0;non_cancer_nhomalt_oth_female=0;AC_nfe_bgr=0;AN_nfe_bgr=308;AF_nfe_bgr=0;nhomalt_nfe_bgr=0;non_neuro_AC_asj_female=0;non_neuro_AN_asj_female=216;non_neuro_AF_asj_female=0;non_neuro_nhomalt_asj_female=0;AC_sas_male=0;AN_sas_male=2492;AF_sas_male=0;nhomalt_sas_male=0;non_neuro_AC_afr_male=0;non_neuro_AN_afr_male=780;non_neuro_AF_afr_male=0;non_neuro_nhomalt_afr_male=0;AC_afr_male=0;AN_afr_male=784;AF_afr_male=0;nhomalt_afr_male=0;AC_afr=0;AN_afr=1658;AF_afr=0;nhomalt_afr=0;controls_AC_nfe_swe=0;controls_AN_nfe_swe=258;controls_AF_nfe_swe=0;controls_nhomalt_nfe_swe=0;non_neuro_AC_afr_female=0;non_neuro_AN_afr_female=870;non_neuro_AF_afr_female=0;non_neuro_nhomalt_afr_female=0;non_topmed_AC_amr_female=0;non_topmed_AN_amr_female=2644;non_topmed_AF_amr_female=0;non_topmed_nhomalt_amr_female=0;non_cancer_AC_female=0;non_cancer_AN_female=15002;non_cancer_AF_female=0;non_cancer_nhomalt_female=0;non_cancer_AC_nfe_onf=0;non_cancer_AN_nfe_onf=1968;non_cancer_AF_nfe_onf=0;non_cancer_nhomalt_nfe_onf=0;non_cancer_AC_male=1;non_cancer_AN_male=16252;non_cancer_AF_male=6.15309e-05;non_cancer_nhomalt_male=0;non_topmed_AC_oth_female=0;non_topmed_AN_oth_female=330;non_topmed_AF_oth_female=0;non_topmed_nhomalt_oth_female=0;AC_eas_female=0;AN_eas_female=962;AF_eas_female=0;nhomalt_eas_female=0;non_cancer_AC_sas_female=0;non_cancer_AN_sas_female=856;non_cancer_AF_sas_female=0;non_cancer_nhomalt_sas_female=0;AC_afr_female=0;AN_afr_female=874;AF_afr_female=0;nhomalt_afr_female=0;AC_sas=0;AN_sas=3354;AF_sas=0;nhomalt_sas=0;non_neuro_AC_female=0;non_neuro_AN_female=13322;non_neuro_AF_female=0;non_neuro_nhomalt_female=0;controls_AC_afr=0;controls_AN_afr=744;controls_AF_afr=0;controls_nhomalt_afr=0;non_neuro_AC_eas_jpn=0;non_neuro_AN_eas_jpn=24;non_neuro_AF_eas_jpn=0;non_neuro_nhomalt_eas_jpn=0;AC_nfe_onf=0;AN_nfe_onf=2698;AF_nfe_onf=0;nhomalt_nfe_onf=0;non_cancer_AC_amr_male=0;non_cancer_AN_amr_male=1974;non_cancer_AF_amr_male=0;non_cancer_nhomalt_amr_male=0;controls_AC_fin_male=1;controls_AN_fin_male=4686;controls_AF_fin_male=0.000213402;controls_nhomalt_fin_male=0;non_neuro_AC_nfe_nwe=0;non_neuro_AN_nfe_nwe=2326;non_neuro_AF_nfe_nwe=0;non_neuro_nhomalt_nfe_nwe=0;AC_fin_male=1;AN_fin_male=5204;AF_fin_male=0.00019216;nhomalt_fin_male=0;AC_nfe_female=0;AN_nfe_female=3914;AF_nfe_female=0;nhomalt_nfe_female=0;AC_amr=0;AN_amr=4648;AF_amr=0;nhomalt_amr=0;non_topmed_AC_nfe_male=0;non_topmed_AN_nfe_male=4716;non_topmed_AF_nfe_male=0;non_topmed_nhomalt_nfe_male=0;non_neuro_AC_sas=0;non_neuro_AN_sas=3354;non_neuro_AF_sas=0;non_neuro_nhomalt_sas=0;non_cancer_AC_fin_male=1;non_cancer_AN_fin_male=5202;non_cancer_AF_fin_male=0.000192234;non_cancer_nhomalt_fin_male=0;non_cancer_AC_nfe_seu=0;non_cancer_AN_nfe_seu=468;non_cancer_AF_nfe_seu=0;non_cancer_nhomalt_nfe_seu=0;AC_eas=0;AN_eas=2090;AF_eas=0;nhomalt_eas=0;nhomalt=0;non_neuro_AC_nfe_female=0;non_neuro_AN_nfe_female=2548;non_neuro_AF_nfe_female=0;non_neuro_nhomalt_nfe_female=0;non_neuro_AC_afr=0;non_neuro_AN_afr=1650;non_neuro_AF_afr=0;non_neuro_nhomalt_afr=0;controls_AC_raw=8;controls_AN_raw=101854;controls_AF_raw=7.85438e-05;controls_nhomalt_raw=0;non_cancer_AC_eas=0;non_cancer_AN_eas=1980;non_cancer_AF_eas=0;non_cancer_nhomalt_eas=0;non_cancer_AC_amr_female=0;non_cancer_AN_amr_female=2630;non_cancer_AF_amr_female=0;non_cancer_nhomalt_amr_female=0;non_neuro_AC_nfe_swe=0;non_neuro_AN_nfe_swe=560;non_neuro_AF_nfe_swe=0;non_neuro_nhomalt_nfe_swe=0;controls_AC_male=1;controls_AN_male=8666;controls_AF_male=0.000115393;controls_nhomalt_male=0;non_topmed_AC_male=1;non_topmed_AN_male=17140;non_topmed_AF_male=5.83431e-05;non_topmed_nhomalt_male=0;controls_AC_eas_jpn=0;controls_AN_eas_jpn=22;controls_AF_eas_jpn=0;controls_nhomalt_eas_jpn=0;controls_AC_nfe_female=0;controls_AN_nfe_female=738;controls_AF_nfe_female=0;controls_nhomalt_nfe_female=0;non_neuro_AC_amr=0;non_neuro_AN_amr=3768;non_neuro_AF_amr=0;non_neuro_nhomalt_amr=0;non_neuro_AC_eas_female=0;non_neuro_AN_eas_female=680;non_neuro_AF_eas_female=0;non_neuro_nhomalt_eas_female=0;AC_asj_male=0;AN_asj_male=562;AF_asj_male=0;nhomalt_asj_male=0;controls_AC_nfe_male=0;controls_AN_nfe_male=774;controls_AF_nfe_male=0;controls_nhomalt_nfe_male=0;non_neuro_AC_fin=1;non_neuro_AN_fin=10754;non_neuro_AF_fin=9.29887e-05;non_neuro_nhomalt_fin=0;non_topmed_AC_sas=0;non_topmed_AN_sas=3354;non_topmed_AF_sas=0;non_topmed_nhomalt_sas=0;non_cancer_AC_nfe_female=0;non_cancer_AN_nfe_female=3316;non_cancer_AF_nfe_female=0;non_cancer_nhomalt_nfe_female=0;AC_oth_female=0;AN_oth_female=330;AF_oth_female=0;nhomalt_oth_female=0;non_cancer_AC_asj=0;non_cancer_AN_asj=882;non_cancer_AF_asj=0;non_cancer_nhomalt_asj=0;AC_nfe_swe=0;AN_nfe_swe=1092;AF_nfe_swe=0;nhomalt_nfe_swe=0;controls_AC_nfe=0;controls_AN_nfe=1512;controls_AF_nfe=0;controls_nhomalt_nfe=0;controls_AC_oth_female=0;controls_AN_oth_female=96;controls_AF_oth_female=0;controls_nhomalt_oth_female=0;controls_AC_asj=0;controls_AN_asj=126;controls_AF_asj=0;controls_nhomalt_asj=0;non_neuro_AC_amr_male=0;non_neuro_AN_amr_male=1546;non_neuro_AF_amr_male=0;non_neuro_nhomalt_amr_male=0;controls_AC_nfe_nwe=0;controls_AN_nfe_nwe=694;controls_AF_nfe_nwe=0;controls_nhomalt_nfe_nwe=0;AC_nfe_nwe=0;AN_nfe_nwe=3924;AF_nfe_nwe=0;nhomalt_nfe_nwe=0;controls_AC_nfe_seu=0;controls_AN_nfe_seu=150;controls_AF_nfe_seu=0;controls_nhomalt_nfe_seu=0;controls_AC_sas_female=0;controls_AN_sas_female=434;controls_AF_sas_female=0;controls_nhomalt_sas_female=0;non_neuro_AC_amr_female=0;non_neuro_AN_amr_female=2222;non_neuro_AF_amr_female=0;non_neuro_nhomalt_amr_female=0;non_cancer_AC_eas_jpn=0;non_cancer_AN_eas_jpn=24;non_cancer_AF_eas_jpn=0;non_cancer_nhomalt_eas_jpn=0;non_neuro_AC_nfe_onf=0;non_neuro_AN_nfe_onf=2010;non_neuro_AF_nfe_onf=0;non_neuro_nhomalt_nfe_onf=0;non_topmed_AC_eas_male=0;non_topmed_AN_eas_male=1128;non_topmed_AF_eas_male=0;non_topmed_nhomalt_eas_male=0;AC_eas_jpn=0;AN_eas_jpn=24;AF_eas_jpn=0;nhomalt_eas_jpn=0;non_cancer_AC_afr_male=0;non_cancer_AN_afr_male=706;non_cancer_AF_afr_male=0;non_cancer_nhomalt_afr_male=0;non_cancer_AC_afr=0;non_cancer_AN_afr=1514;non_cancer_AF_afr=0;non_cancer_nhomalt_afr=0;controls_AC_amr_female=0;controls_AN_amr_female=1428;controls_AF_amr_female=0;controls_nhomalt_amr_female=0;non_neuro_AC_fin_male=1;non_neuro_AN_fin_male=5104;non_neuro_AF_fin_male=0.000195925;non_neuro_nhomalt_fin_male=0;AC_female=0;AN_female=15790;AF_female=0;nhomalt_female=0;non_neuro_AC_nfe_bgr=0;non_neuro_AN_nfe_bgr=50;non_neuro_AF_nfe_bgr=0;non_neuro_nhomalt_nfe_bgr=0;non_neuro_AC_oth_male=0;non_neuro_AN_oth_male=302;non_neuro_AF_oth_male=0;non_neuro_nhomalt_oth_male=0;non_topmed_AC_nfe_est=0;non_topmed_AN_nfe_est=36;non_topmed_AF_nfe_est=0;non_topmed_nhomalt_nfe_est=0;non_topmed_AC_nfe_nwe=0;non_topmed_AN_nfe_nwe=3876;non_topmed_AF_nfe_nwe=0;non_topmed_nhomalt_nfe_nwe=0;non_topmed_AC_amr_male=0;non_topmed_AN_amr_male=1990;non_topmed_AF_amr_male=0;non_topmed_nhomalt_amr_male=0;non_cancer_AC_amr=0;non_cancer_AN_amr=4604;non_cancer_AF_amr=0;non_cancer_nhomalt_amr=0;non_topmed_AC_nfe_swe=0;non_topmed_AN_nfe_swe=1086;non_topmed_AF_nfe_swe=0;non_topmed_nhomalt_nfe_swe=0;non_topmed_AC_nfe_onf=0;non_topmed_AN_nfe_onf=2678;non_topmed_AF_nfe_onf=0;non_topmed_nhomalt_nfe_onf=0;controls_AC_eas_kor=0;controls_AN_eas_kor=208;controls_AF_eas_kor=0;controls_nhomalt_eas_kor=0;non_topmed_AC_eas_oea=0;non_topmed_AN_eas_oea=1630;non_topmed_AF_eas_oea=0;non_topmed_nhomalt_eas_oea=0;controls_AC_eas_male=0;controls_AN_eas_male=536;controls_AF_eas_male=0;controls_nhomalt_eas_male=0;controls_AC_oth_male=0;controls_AN_oth_male=98;controls_AF_oth_male=0;controls_nhomalt_oth_male=0;non_topmed_AC=1;non_topmed_AN=32730;non_topmed_AF=3.0553e-05;non_topmed_nhomalt=0;controls_AC_fin=1;controls_AN_fin=9966;controls_AF_fin=0.000100341;controls_nhomalt_fin=0;AC_eas_kor=0;AN_eas_kor=436;AF_eas_kor=0;nhomalt_eas_kor=0;non_neuro_AC_nfe=0;non_neuro_AN_nfe=5450;non_neuro_AF_nfe=0;non_neuro_nhomalt_nfe=0;non_neuro_AC_fin_female=0;non_neuro_AN_fin_female=5650;non_neuro_AF_fin_female=0;non_neuro_nhomalt_fin_female=0;non_cancer_AC_nfe_male=0;non_cancer_AN_nfe_male=3974;non_cancer_AF_nfe_male=0;non_cancer_nhomalt_nfe_male=0;controls_AC_eas_oea=0;controls_AN_eas_oea=772;controls_AF_eas_oea=0;controls_nhomalt_eas_oea=0;non_topmed_AC_nfe_seu=0;non_topmed_AN_nfe_seu=598;non_topmed_AF_nfe_seu=0;non_topmed_nhomalt_nfe_seu=0;controls_AC_eas_female=0;controls_AN_eas_female=466;controls_AF_eas_female=0;controls_nhomalt_eas_female=0;non_topmed_AC_asj=0;non_topmed_AN_asj=970;non_topmed_AF_asj=0;non_topmed_nhomalt_asj=0;controls_AC_nfe_onf=0;controls_AN_nfe_onf=384;controls_AF_nfe_onf=0;controls_nhomalt_nfe_onf=0;non_neuro_AC=1;non_neuro_AN=27590;non_neuro_AF=3.6245e-05;non_neuro_nhomalt=0;AC_eas_oea=0;AN_eas_oea=1630;AF_eas_oea=0;nhomalt_eas_oea=0;non_topmed_AC_nfe=0;non_topmed_AN_nfe=8582;non_topmed_AF_nfe=0;non_topmed_nhomalt_nfe=0;non_cancer_AC_oth=0;non_cancer_AN_oth=656;non_cancer_AF_oth=0;non_cancer_nhomalt_oth=0;non_topmed_AC_raw=10;non_topmed_AN_raw=226612;non_topmed_AF_raw=4.41283e-05;non_topmed_nhomalt_raw=0;non_neuro_AC_nfe_est=0;non_neuro_AN_nfe_est=30;non_neuro_AF_nfe_est=0;non_neuro_nhomalt_nfe_est=0;non_topmed_AC_oth_male=0;non_topmed_AN_oth_male=382;non_topmed_AF_oth_male=0;non_topmed_nhomalt_oth_male=0;non_cancer_AC_oth_male=0;non_cancer_AN_oth_male=352;non_cancer_AF_oth_male=0;non_cancer_nhomalt_oth_male=0;AC_nfe_est=0;AN_nfe_est=36;AF_nfe_est=0;nhomalt_nfe_est=0;non_cancer_AC_afr_female=0;non_cancer_AN_afr_female=808;non_cancer_AF_afr_female=0;non_cancer_nhomalt_afr_female=0;non_topmed_AC_afr_male=0;non_topmed_AN_afr_male=670;non_topmed_AF_afr_male=0;non_topmed_nhomalt_afr_male=0;AC_eas_male=0;AN_eas_male=1128;AF_eas_male=0;nhomalt_eas_male=0;controls_AC_eas=0;controls_AN_eas=1002;controls_AF_eas=0;controls_nhomalt_eas=0;non_neuro_AC_eas_male=0;non_neuro_AN_eas_male=840;non_neuro_AF_eas_male=0;non_neuro_nhomalt_eas_male=0;non_cancer_AC_nfe_nwe=0;non_cancer_AN_nfe_nwe=3508;non_cancer_AF_nfe_nwe=0;non_cancer_nhomalt_nfe_nwe=0;controls_AC_sas=0;controls_AN_sas=1558;controls_AF_sas=0;controls_nhomalt_sas=0;non_neuro_AC_sas_male=0;non_neuro_AN_sas_male=2492;non_neuro_AF_sas_male=0;non_neuro_nhomalt_sas_male=0;non_neuro_AC_asj_male=0;non_neuro_AN_asj_male=302;non_neuro_AF_asj_male=0;non_neuro_nhomalt_asj_male=0;non_cancer_AC_nfe_bgr=0;non_cancer_AN_nfe_bgr=290;non_cancer_AF_nfe_bgr=0;non_cancer_nhomalt_nfe_bgr=0;controls_AC_oth=0;controls_AN_oth=194;controls_AF_oth=0;controls_nhomalt_oth=0;non_cancer_AC_eas_female=0;non_cancer_AN_eas_female=932;non_cancer_AF_eas_female=0;non_cancer_nhomalt_eas_female=0;AC_nfe=0;AN_nfe=8660;AF_nfe=0;nhomalt_nfe=0;non_topmed_AC_female=0;non_topmed_AN_female=15590;non_topmed_AF_female=0;non_topmed_nhomalt_female=0;non_neuro_AC_asj=0;non_neuro_AN_asj=518;non_neuro_AF_asj=0;non_neuro_nhomalt_asj=0;non_topmed_AC_eas_female=0;non_topmed_AN_eas_female=962;non_topmed_AF_eas_female=0;non_topmed_nhomalt_eas_female=0;non_neuro_AC_raw=10;non_neuro_AN_raw=191928;non_neuro_AF_raw=5.21029e-05;non_neuro_nhomalt_raw=0;non_topmed_AC_eas=0;non_topmed_AN_eas=2090;non_topmed_AF_eas=0;non_topmed_nhomalt_eas=0;non_topmed_AC_fin_male=1;non_topmed_AN_fin_male=5204;non_topmed_AF_fin_male=0.00019216;non_topmed_nhomalt_fin_male=0;non_cancer_AC_asj_male=0;non_cancer_AN_asj_male=506;non_cancer_AF_asj_male=0;non_cancer_nhomalt_asj_male=0;AC_fin=1;AN_fin=10984;AF_fin=9.10415e-05;nhomalt_fin=0;AC_nfe_male=0;AN_nfe_male=4746;AF_nfe_male=0;nhomalt_nfe_male=0;non_topmed_AC_eas_kor=0;non_topmed_AN_eas_kor=436;non_topmed_AF_eas_kor=0;non_topmed_nhomalt_eas_kor=0;controls_AC_amr_male=0;controls_AN_amr_male=1010;controls_AF_amr_male=0;controls_nhomalt_amr_male=0;non_neuro_AC_eas_oea=0;non_neuro_AN_eas_oea=1060;non_neuro_AF_eas_oea=0;non_neuro_nhomalt_eas_oea=0;AC_sas_female=0;AN_sas_female=862;AF_sas_female=0;nhomalt_sas_female=0;controls_AC_afr_female=0;controls_AN_afr_female=388;controls_AF_afr_female=0;controls_nhomalt_afr_female=0;controls_AC_amr=0;controls_AN_amr=2438;controls_AF_amr=0;controls_nhomalt_amr=0;non_topmed_AC_eas_jpn=0;non_topmed_AN_eas_jpn=24;non_topmed_AF_eas_jpn=0;non_topmed_nhomalt_eas_jpn=0;AC_asj_female=0;AN_asj_female=412;AF_asj_female=0;nhomalt_asj_female=0;non_topmed_AC_nfe_bgr=0;non_topmed_AN_nfe_bgr=308;non_topmed_AF_nfe_bgr=0;non_topmed_nhomalt_nfe_bgr=0;non_cancer_AC_nfe_est=0;non_cancer_AN_nfe_est=18;non_cancer_AF_nfe_est=0;non_cancer_nhomalt_nfe_est=0;non_neuro_AC_eas=0;non_neuro_AN_eas=1520;non_neuro_AF_eas=0;non_neuro_nhomalt_eas=0;non_cancer_AC_nfe=0;non_cancer_AN_nfe=7290;non_cancer_AF_nfe=0;non_cancer_nhomalt_nfe=0;non_neuro_AC_male=1;non_neuro_AN_male=14268;non_neuro_AF_male=7.00869e-05;non_neuro_nhomalt_male=0;non_neuro_AC_sas_female=0;non_neuro_AN_sas_female=862;non_neuro_AF_sas_female=0;non_neuro_nhomalt_sas_female=0;AC_asj=0;AN_asj=974;AF_asj=0;nhomalt_asj=0;controls_AC_nfe_est=0;controls_AN_nfe_est=8;controls_AF_nfe_est=0;controls_nhomalt_nfe_est=0;non_topmed_AC_asj_female=0;non_topmed_AN_asj_female=412;non_topmed_AF_asj_female=0;non_topmed_nhomalt_asj_female=0;non_cancer_AC_nfe_swe=0;non_cancer_AN_nfe_swe=1038;non_cancer_AF_nfe_swe=0;non_cancer_nhomalt_nfe_swe=0;non_cancer_AC=1;non_cancer_AN=31254;non_cancer_AF=3.19959e-05;non_cancer_nhomalt=0;non_topmed_AC_oth=0;non_topmed_AN_oth=712;non_topmed_AF_oth=0;non_topmed_nhomalt_oth=0;non_topmed_AC_fin_female=0;non_topmed_AN_fin_female=5780;non_topmed_AF_fin_female=0;non_topmed_nhomalt_fin_female=0;non_cancer_AC_fin_female=0;non_cancer_AN_fin_female=5780;non_cancer_AF_fin_female=0;non_cancer_nhomalt_fin_female=0;AC_oth=0;AN_oth=714;AF_oth=0;nhomalt_oth=0;non_neuro_AC_nfe_male=0;non_neuro_AN_nfe_male=2902;non_neuro_AF_nfe_male=0;non_neuro_nhomalt_nfe_male=0;controls_AC_female=0;controls_AN_female=8874;controls_AF_female=0;controls_nhomalt_female=0;non_cancer_AC_fin=1;non_cancer_AN_fin=10982;non_cancer_AF_fin=9.10581e-05;non_cancer_nhomalt_fin=0;non_topmed_AC_fin=1;non_topmed_AN_fin=10984;non_topmed_AF_fin=9.10415e-05;non_topmed_nhomalt_fin=0;non_cancer_AC_eas_oea=0;non_cancer_AN_eas_oea=1528;non_cancer_AF_eas_oea=0;non_cancer_nhomalt_eas_oea=0;non_topmed_AC_nfe_female=0;non_topmed_AN_nfe_female=3866;non_topmed_AF_nfe_female=0;non_topmed_nhomalt_nfe_female=0;non_cancer_AC_sas_male=0;non_cancer_AN_sas_male=2490;non_cancer_AF_sas_male=0;non_cancer_nhomalt_sas_male=0;controls_AC_asj_male=0;controls_AN_asj_male=82;controls_AF_asj_male=0;controls_nhomalt_asj_male=0;non_cancer_AC_raw=10;non_cancer_AN_raw=221656;non_cancer_AF_raw=4.5115e-05;non_cancer_nhomalt_raw=0;non_cancer_AC_eas_male=0;non_cancer_AN_eas_male=1048;non_cancer_AF_eas_male=0;non_cancer_nhomalt_eas_male=0;non_topmed_AC_asj_male=0;non_topmed_AN_asj_male=558;non_topmed_AF_asj_male=0;non_topmed_nhomalt_asj_male=0;non_neuro_AC_oth=0;non_neuro_AN_oth=576;non_neuro_AF_oth=0;non_neuro_nhomalt_oth=0;AC_male=1;AN_male=17292;AF_male=5.78302e-05;nhomalt_male=0;controls_AC_fin_female=0;controls_AN_fin_female=5280;controls_AF_fin_female=0;controls_nhomalt_fin_female=0;controls_AC_nfe_bgr=0;controls_AN_nfe_bgr=18;controls_AF_nfe_bgr=0;controls_nhomalt_nfe_bgr=0;controls_AC_asj_female=0;controls_AN_asj_female=44;controls_AF_asj_female=0;controls_nhomalt_asj_female=0;AC_amr_male=0;AN_amr_male=1992;AF_amr_male=0;nhomalt_amr_male=0;AC_amr_female=0;AN_amr_female=2656;AF_amr_female=0;nhomalt_amr_female=0;non_topmed_AC_sas_male=0;non_topmed_AN_sas_male=2492;non_topmed_AF_sas_male=0;non_topmed_nhomalt_sas_male=0;AC_oth_male=0;AN_oth_male=384;AF_oth_male=0;nhomalt_oth_male=0;non_cancer_AC_sas=0;non_cancer_AN_sas=3346;non_cancer_AF_sas=0;non_cancer_nhomalt_sas=0;non_neuro_AC_nfe_seu=0;non_neuro_AN_nfe_seu=474;non_neuro_AF_nfe_seu=0;non_neuro_nhomalt_nfe_seu=0;non_cancer_AC_eas_kor=0;non_cancer_AN_eas_kor=428;non_cancer_AF_eas_kor=0;non_cancer_nhomalt_eas_kor=0;non_topmed_AC_afr_female=0;non_topmed_AN_afr_female=734;non_topmed_AF_afr_female=0;non_topmed_nhomalt_afr_female=0;controls_AC_sas_male=0;controls_AN_sas_male=1124;controls_AF_sas_male=0;controls_nhomalt_sas_male=0;non_topmed_AC_sas_female=0;non_topmed_AN_sas_female=862;non_topmed_AF_sas_female=0;non_topmed_nhomalt_sas_female=0;non_topmed_AC_afr=0;non_topmed_AN_afr=1404;non_topmed_AF_afr=0;non_topmed_nhomalt_afr=0;controls_AC=1;controls_AN=17540;controls_AF=5.70125e-05;controls_nhomalt=0;non_neuro_AC_oth_female=0;non_neuro_AN_oth_female=274;non_neuro_AF_oth_female=0;non_neuro_nhomalt_oth_female=0;non_topmed_faf95_amr=0;non_topmed_faf99_amr=0;faf95_afr=0;faf99_afr=0;faf95_sas=0;faf99_sas=0;controls_faf95_afr=0;controls_faf99_afr=0;faf95_amr=0;faf99_amr=0;non_neuro_faf95_sas=0;non_neuro_faf99_sas=0;faf95_eas=0;faf99_eas=0;faf95=0;faf99=0;non_neuro_faf95_afr=0;non_neuro_faf99_afr=0;non_cancer_faf95_eas=0;non_cancer_faf99_eas=0;non_neuro_faf95_amr=0;non_neuro_faf99_amr=0;non_topmed_faf95_sas=0;non_topmed_faf99_sas=0;controls_faf95_nfe=0;controls_faf99_nfe=0;non_cancer_faf95_afr=0;non_cancer_faf99_afr=0;non_cancer_faf95_amr=0;non_cancer_faf99_amr=0;non_topmed_faf95=0;non_topmed_faf99=0;non_neuro_faf95_nfe=0;non_neuro_faf99_nfe=0;non_neuro_faf95=0;non_neuro_faf99=0;non_topmed_faf95_nfe=0;non_topmed_faf99_nfe=0;controls_faf95_eas=0;controls_faf99_eas=0;controls_faf95_sas=0;controls_faf99_sas=0;faf95_nfe=0;faf99_nfe=0;non_topmed_faf95_eas=0;non_topmed_faf99_eas=0;controls_faf95_amr=0;controls_faf99_amr=0;non_neuro_faf95_eas=0;non_neuro_faf99_eas=0;non_cancer_faf95_nfe=0;non_cancer_faf99_nfe=0;non_cancer_faf95=0;non_cancer_faf99=0;non_cancer_faf95_sas=0;non_cancer_faf99_sas=0;non_topmed_faf95_afr=0;non_topmed_faf99_afr=0;controls_faf95=0;controls_faf99=0;age_hist_het_bin_freq=0|0|0|0|0|0|0|0|0|0;age_hist_het_n_smaller=1;age_hist_het_n_larger=0;age_hist_hom_bin_freq=0|0|0|0|0|0|0|0|0|0;age_hist_hom_n_smaller=0;age_hist_hom_n_larger=0;vep=-|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000309212|protein_coding||2/9|ENST00000309212.6:c.73+41_73+44delTCAG||||||||1||-1||deletion|1|HGNC|7542|YES|||CCDS24.1|ENSP00000307887|Q9BRK3||UPI000003ED26||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000342753|protein_coding||2/8|ENST00000342753.4:c.73+41_73+44delTCAG||||||||1||-1||deletion|1|HGNC|7542||||CCDS59950.1|ENSP00000344998|||UPI00001A7404||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000445648|protein_coding||2/9|ENST00000445648.2:c.73+41_73+44delTCAG||||||||1||-1||deletion|1|HGNC|7542||||CCDS59951.1|ENSP00000399229|Q9BRK3||UPI0000470B85||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000460473|retained_intron|||||||||||1|1125|-1||deletion|1|HGNC|7542||||||||||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000464351|retained_intron|||||||||||1|1125|-1||deletion|1|HGNC|7542||||||||||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000473097|retained_intron|||||||||||1|2163|-1||deletion|1|HGNC|7542||||||||||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000474033|retained_intron|||||||||||1|2373|-1||deletion|1|HGNC|7542||||||||||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000476718|retained_intron|||||||||||1|1621|-1||deletion|1|HGNC|7542||||||||||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000477278|protein_coding||2/9|ENST00000477278.2:c.46+41_46+44delTCAG||||||||1||-1||deletion|1|HGNC|7542||||CCDS59952.1|ENSP00000436135||B3KTR6|UPI000013E183||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000478517|retained_intron|||||||||||1|2390|-1||deletion|1|HGNC|7542||||||||||||||||||||||||||||||||||||||||||
1   11288758    rs1064261   G   GACTCGAATGACA   3.56379e+08 PASS    AC=1;AN=251254;AF=3.98004e-06;rf_tp_probability=0.891093;FS=0.735;InbreedingCoeff=0.0728;MQ=59.5;MQRankSum=0.085;QD=26.64;ReadPosRankSum=0.394;SOR=0.749;BaseQRankSum=2.07;ClippingRankSum=-0.02;DP=14304502;VQSLOD=3.01;VQSR_culprit=FS;variant_type=mixed;allele_type=ins;n_alt_alleles=2;was_mixed;pab_max=0.742829;gq_hist_alt_bin_freq=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;gq_hist_all_bin_freq=11|9|7|12|23|19|32|49|31|75|101|80|161|221|184|331|540|270|793|122799;dp_hist_alt_bin_freq=0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0|0|0;dp_hist_alt_n_larger=0;dp_hist_all_bin_freq=8|56|144|286|630|1529|3560|7389|9291|10832|11946|11750|10400|8662|7249|5921|5099|4251|3676|3769;dp_hist_all_n_larger=19300;ab_hist_alt_bin_freq=0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0;AC_nfe_seu=0;AN_nfe_seu=11472;AF_nfe_seu=0;nhomalt_nfe_seu=0;controls_AC_afr_male=0;controls_AN_afr_male=2924;controls_AF_afr_male=0;controls_nhomalt_afr_male=0;non_neuro_AC_eas_kor=0;non_neuro_AN_eas_kor=3816;non_neuro_AF_eas_kor=0;non_neuro_nhomalt_eas_kor=0;non_topmed_AC_amr=0;non_topmed_AN_amr=34436;non_topmed_AF_amr=0;non_topmed_nhomalt_amr=0;non_cancer_AC_asj_female=0;non_cancer_AN_asj_female=4590;non_cancer_AF_asj_female=0;non_cancer_nhomalt_asj_female=0;AC_raw=1;AN_raw=251496;AF_raw=3.97621e-06;nhomalt_raw=0;AC_fin_female=0;AN_fin_female=10364;AF_fin_female=0;nhomalt_fin_female=0;non_cancer_AC_oth_female=0;non_cancer_AN_oth_female=2682;non_cancer_AF_oth_female=0;non_cancer_nhomalt_oth_female=0;AC_nfe_bgr=0;AN_nfe_bgr=2664;AF_nfe_bgr=0;nhomalt_nfe_bgr=0;non_neuro_AC_asj_female=0;non_neuro_AN_asj_female=3082;non_neuro_AF_asj_female=0;non_neuro_nhomalt_asj_female=0;AC_sas_male=0;AN_sas_male=23072;AF_sas_male=0;nhomalt_sas_male=0;non_neuro_AC_afr_male=0;non_neuro_AN_afr_male=6164;non_neuro_AF_afr_male=0;non_neuro_nhomalt_afr_male=0;AC_afr_male=0;AN_afr_male=6186;AF_afr_male=0;nhomalt_afr_male=0;AC_afr=0;AN_afr=16252;AF_afr=0;nhomalt_afr=0;controls_AC_nfe_swe=0;controls_AN_nfe_swe=12808;controls_AF_nfe_swe=0;controls_nhomalt_nfe_swe=0;non_neuro_AC_afr_female=0;non_neuro_AN_afr_female=10050;non_neuro_AF_afr_female=0;non_neuro_nhomalt_afr_female=0;non_topmed_AC_amr_female=0;non_topmed_AN_amr_female=20184;non_topmed_AF_amr_female=0;non_topmed_nhomalt_amr_female=0;non_cancer_AC_female=0;non_cancer_AN_female=107594;non_cancer_AF_female=0;non_cancer_nhomalt_female=0;non_cancer_AC_nfe_onf=0;non_cancer_AN_nfe_onf=24616;non_cancer_AF_nfe_onf=0;non_cancer_nhomalt_nfe_onf=0;non_cancer_AC_male=1;non_cancer_AN_male=129128;non_cancer_AF_male=7.74425e-06;non_cancer_nhomalt_male=0;non_topmed_AC_oth_female=0;non_topmed_AN_oth_female=2878;non_topmed_AF_oth_female=0;non_topmed_nhomalt_oth_female=0;AC_eas_female=0;AN_eas_female=9328;AF_eas_female=0;nhomalt_eas_female=0;non_cancer_AC_sas_female=0;non_cancer_AN_sas_female=7494;non_cancer_AF_sas_female=0;non_cancer_nhomalt_sas_female=0;AC_afr_female=0;AN_afr_female=10066;AF_afr_female=0;nhomalt_afr_female=0;AC_sas=0;AN_sas=30616;AF_sas=0;nhomalt_sas=0;non_neuro_AC_female=0;non_neuro_AN_female=95614;non_neuro_AF_female=0;non_neuro_nhomalt_female=0;controls_AC_afr=0;controls_AN_afr=7162;controls_AF_afr=0;controls_nhomalt_afr=0;non_neuro_AC_eas_jpn=0;non_neuro_AN_eas_jpn=150;non_neuro_AF_eas_jpn=0;non_neuro_nhomalt_eas_jpn=0;AC_nfe_onf=0;AN_nfe_onf=30946;AF_nfe_onf=0;nhomalt_nfe_onf=0;non_cancer_AC_amr_male=0;non_cancer_AN_amr_male=14162;non_cancer_AF_amr_male=0;non_cancer_nhomalt_amr_male=0;controls_AC_fin_male=0;controls_AN_fin_male=6916;controls_AF_fin_male=0;controls_nhomalt_fin_male=0;non_neuro_AC_nfe_nwe=0;non_neuro_AN_nfe_nwe=35342;non_neuro_AF_nfe_nwe=0;non_neuro_nhomalt_nfe_nwe=0;AC_fin_male=1;AN_fin_male=11262;AF_fin_male=8.87942e-05;nhomalt_fin_male=0;AC_nfe_female=0;AN_nfe_female=50078;AF_nfe_female=0;nhomalt_nfe_female=0;AC_amr=0;AN_amr=34570;AF_amr=0;nhomalt_amr=0;non_topmed_AC_nfe_male=0;non_topmed_AN_nfe_male=62774;non_topmed_AF_nfe_male=0;non_topmed_nhomalt_nfe_male=0;non_neuro_AC_sas=0;non_neuro_AN_sas=30608;non_neuro_AF_sas=0;non_neuro_nhomalt_sas=0;non_cancer_AC_fin_male=1;non_cancer_AN_fin_male=11258;non_cancer_AF_fin_male=8.88257e-05;non_cancer_nhomalt_fin_male=0;non_cancer_AC_nfe_seu=0;non_cancer_AN_nfe_seu=10580;non_cancer_AF_nfe_seu=0;non_cancer_nhomalt_nfe_seu=0;AC_eas=0;AN_eas=18392;AF_eas=0;nhomalt_eas=0;nhomalt=0;non_neuro_AC_nfe_female=0;non_neuro_AN_nfe_female=39802;non_neuro_AF_nfe_female=0;non_neuro_nhomalt_nfe_female=0;non_neuro_AC_afr=0;non_neuro_AN_afr=16214;non_neuro_AF_afr=0;non_neuro_nhomalt_afr=0;controls_AC_raw=0;controls_AN_raw=109408;controls_AF_raw=0;controls_nhomalt_raw=0;non_cancer_AC_eas=0;non_cancer_AN_eas=17690;non_cancer_AF_eas=0;non_cancer_nhomalt_eas=0;non_cancer_AC_amr_female=0;non_cancer_AN_amr_female=20076;non_cancer_AF_amr_female=0;non_cancer_nhomalt_amr_female=0;non_neuro_AC_nfe_swe=0;non_neuro_AN_nfe_swe=14778;non_neuro_AF_nfe_swe=0;non_neuro_nhomalt_nfe_swe=0;controls_AC_male=0;controls_AN_male=58094;controls_AF_male=0;controls_nhomalt_male=0;non_topmed_AC_male=1;non_topmed_AN_male=133424;non_topmed_AF_male=7.4949e-06;non_topmed_nhomalt_male=0;controls_AC_eas_jpn=0;controls_AN_eas_jpn=114;controls_AF_eas_jpn=0;controls_nhomalt_eas_jpn=0;controls_AC_nfe_female=0;controls_AN_nfe_female=19138;controls_AF_nfe_female=0;controls_nhomalt_nfe_female=0;non_neuro_AC_amr=0;non_neuro_AN_amr=30504;non_neuro_AF_amr=0;non_neuro_nhomalt_amr=0;non_neuro_AC_eas_female=0;non_neuro_AN_eas_female=6842;non_neuro_AF_eas_female=0;non_neuro_nhomalt_eas_female=0;AC_asj_male=0;AN_asj_male=5178;AF_asj_male=0;nhomalt_asj_male=0;controls_AC_nfe_male=0;controls_AN_nfe_male=23606;controls_AF_nfe_male=0;controls_nhomalt_nfe_male=0;non_neuro_AC_fin=1;non_neuro_AN_fin=16730;non_neuro_AF_fin=5.97729e-05;non_neuro_nhomalt_fin=0;non_topmed_AC_sas=0;non_topmed_AN_sas=30616;non_topmed_AF_sas=0;non_topmed_nhomalt_sas=0;non_cancer_AC_nfe_female=0;non_cancer_AN_nfe_female=44226;non_cancer_AF_nfe_female=0;non_cancer_nhomalt_nfe_female=0;AC_oth_female=0;AN_oth_female=2928;AF_oth_female=0;nhomalt_oth_female=0;non_cancer_AC_asj=0;non_cancer_AN_asj=9564;non_cancer_AF_asj=0;non_cancer_nhomalt_asj=0;AC_nfe_swe=0;AN_nfe_swe=26124;AF_nfe_swe=0;nhomalt_nfe_swe=0;controls_AC_nfe=0;controls_AN_nfe=42744;controls_AF_nfe=0;controls_nhomalt_nfe=0;controls_AC_oth_female=0;controls_AN_oth_female=986;controls_AF_oth_female=0;controls_nhomalt_oth_female=0;controls_AC_asj=0;controls_AN_asj=2320;controls_AF_asj=0;controls_nhomalt_asj=0;non_neuro_AC_amr_male=0;non_neuro_AN_amr_male=12248;non_neuro_AF_amr_male=0;non_neuro_nhomalt_amr_male=0;controls_AC_nfe_nwe=0;controls_AN_nfe_nwe=14446;controls_AF_nfe_nwe=0;controls_nhomalt_nfe_nwe=0;AC_nfe_nwe=0;AN_nfe_nwe=42148;AF_nfe_nwe=0;nhomalt_nfe_nwe=0;controls_AC_nfe_seu=0;controls_AN_nfe_seu=4746;controls_AF_nfe_seu=0;controls_nhomalt_nfe_seu=0;controls_AC_sas_female=0;controls_AN_sas_female=4214;controls_AF_sas_female=0;controls_nhomalt_sas_female=0;non_neuro_AC_amr_female=0;non_neuro_AN_amr_female=18256;non_neuro_AF_amr_female=0;non_neuro_nhomalt_amr_female=0;non_cancer_AC_eas_jpn=0;non_cancer_AN_eas_jpn=124;non_cancer_AF_eas_jpn=0;non_cancer_nhomalt_eas_jpn=0;non_neuro_AC_nfe_onf=0;non_neuro_AN_nfe_onf=27798;non_neuro_AF_nfe_onf=0;non_neuro_nhomalt_nfe_onf=0;non_topmed_AC_eas_male=0;non_topmed_AN_eas_male=9060;non_topmed_AF_eas_male=0;non_topmed_nhomalt_eas_male=0;AC_eas_jpn=0;AN_eas_jpn=152;AF_eas_jpn=0;nhomalt_eas_jpn=0;non_cancer_AC_afr_male=0;non_cancer_AN_afr_male=5672;non_cancer_AF_afr_male=0;non_cancer_nhomalt_afr_male=0;non_cancer_AC_afr=0;non_cancer_AN_afr=14898;non_cancer_AF_afr=0;non_cancer_nhomalt_afr=0;controls_AC_amr_female=0;controls_AN_amr_female=10224;controls_AF_amr_female=0;controls_nhomalt_amr_female=0;non_neuro_AC_fin_male=1;non_neuro_AN_fin_male=9080;non_neuro_AF_fin_male=0.000110132;non_neuro_nhomalt_fin_male=0;AC_female=0;AN_female=115462;AF_female=0;nhomalt_female=0;non_neuro_AC_nfe_bgr=0;non_neuro_AN_nfe_bgr=448;non_neuro_AF_nfe_bgr=0;non_neuro_nhomalt_nfe_bgr=0;non_neuro_AC_oth_male=0;non_neuro_AN_oth_male=2470;non_neuro_AF_oth_male=0;non_neuro_nhomalt_oth_male=0;non_topmed_AC_nfe_est=0;non_topmed_AN_nfe_est=238;non_topmed_AF_nfe_est=0;non_topmed_nhomalt_nfe_est=0;non_topmed_AC_nfe_nwe=0;non_topmed_AN_nfe_nwe=41028;non_topmed_AF_nfe_nwe=0;non_topmed_nhomalt_nfe_nwe=0;non_topmed_AC_amr_male=0;non_topmed_AN_amr_male=14252;non_topmed_AF_amr_male=0;non_topmed_nhomalt_amr_male=0;non_cancer_AC_amr=0;non_cancer_AN_amr=34238;non_cancer_AF_amr=0;non_cancer_nhomalt_amr=0;non_topmed_AC_nfe_swe=0;non_topmed_AN_nfe_swe=26062;non_topmed_AF_nfe_swe=0;non_topmed_nhomalt_nfe_swe=0;non_topmed_AC_nfe_onf=0;non_topmed_AN_nfe_onf=30146;non_topmed_AF_nfe_onf=0;non_topmed_nhomalt_nfe_onf=0;controls_AC_eas_kor=0;controls_AN_eas_kor=1888;controls_AF_eas_kor=0;controls_nhomalt_eas_kor=0;non_topmed_AC_eas_oea=0;non_topmed_AN_eas_oea=14418;non_topmed_AF_eas_oea=0;non_topmed_nhomalt_eas_oea=0;controls_AC_eas_male=0;controls_AN_eas_male=4256;controls_AF_eas_male=0;controls_nhomalt_eas_male=0;controls_AC_oth_male=0;controls_AN_oth_male=928;controls_AF_oth_male=0;controls_nhomalt_oth_male=0;non_topmed_AC=1;non_topmed_AN=244640;non_topmed_AF=4.08764e-06;non_topmed_nhomalt=0;controls_AC_fin=0;controls_AN_fin=13390;controls_AF_fin=0;controls_nhomalt_fin=0;AC_eas_kor=0;AN_eas_kor=3818;AF_eas_kor=0;nhomalt_eas_kor=0;non_neuro_AC_nfe=0;non_neuro_AN_nfe=89498;non_neuro_AF_nfe=0;non_neuro_nhomalt_nfe=0;non_neuro_AC_fin_female=0;non_neuro_AN_fin_female=7650;non_neuro_AF_fin_female=0;non_neuro_nhomalt_fin_female=0;non_cancer_AC_nfe_male=0;non_cancer_AN_nfe_male=58360;non_cancer_AF_nfe_male=0;non_cancer_nhomalt_nfe_male=0;controls_AC_eas_oea=0;controls_AN_eas_oea=7042;controls_AF_eas_oea=0;controls_nhomalt_eas_oea=0;non_topmed_AC_nfe_seu=0;non_topmed_AN_nfe_seu=11376;non_topmed_AF_nfe_seu=0;non_topmed_nhomalt_nfe_seu=0;controls_AC_eas_female=0;controls_AN_eas_female=4788;controls_AF_eas_female=0;controls_nhomalt_eas_female=0;non_topmed_AC_asj=0;non_topmed_AN_asj=9990;non_topmed_AF_asj=0;non_topmed_nhomalt_asj=0;controls_AC_nfe_onf=0;controls_AN_nfe_onf=9996;controls_AF_nfe_onf=0;controls_nhomalt_nfe_onf=0;non_neuro_AC=1;non_neuro_AN=208036;non_neuro_AF=4.80686e-06;non_neuro_nhomalt=0;AC_eas_oea=0;AN_eas_oea=14422;AF_eas_oea=0;nhomalt_eas_oea=0;non_topmed_AC_nfe=0;non_topmed_AN_nfe=111506;non_topmed_AF_nfe=0;non_topmed_nhomalt_nfe=0;non_cancer_AC_oth=0;non_cancer_AN_oth=5610;non_cancer_AF_oth=0;non_cancer_nhomalt_oth=0;non_topmed_AC_raw=1;non_topmed_AN_raw=244878;non_topmed_AF_raw=4.08367e-06;non_topmed_nhomalt_raw=0;non_neuro_AC_nfe_est=0;non_neuro_AN_nfe_est=216;non_neuro_AF_nfe_est=0;non_neuro_nhomalt_nfe_est=0;non_topmed_AC_oth_male=0;non_topmed_AN_oth_male=3176;non_topmed_AF_oth_male=0;non_topmed_nhomalt_oth_male=0;non_cancer_AC_oth_male=0;non_cancer_AN_oth_male=2928;non_cancer_AF_oth_male=0;non_cancer_nhomalt_oth_male=0;AC_nfe_est=0;AN_nfe_est=242;AF_nfe_est=0;nhomalt_nfe_est=0;non_cancer_AC_afr_female=0;non_cancer_AN_afr_female=9226;non_cancer_AF_afr_female=0;non_cancer_nhomalt_afr_female=0;non_topmed_AC_afr_male=0;non_topmed_AN_afr_male=4686;non_topmed_AF_afr_male=0;non_topmed_nhomalt_afr_male=0;AC_eas_male=0;AN_eas_male=9064;AF_eas_male=0;nhomalt_eas_male=0;controls_AC_eas=0;controls_AN_eas=9044;controls_AF_eas=0;controls_nhomalt_eas=0;non_neuro_AC_eas_male=0;non_neuro_AN_eas_male=6572;non_neuro_AF_eas_male=0;non_neuro_nhomalt_eas_male=0;non_cancer_AC_nfe_nwe=0;non_cancer_AN_nfe_nwe=39430;non_cancer_AF_nfe_nwe=0;non_cancer_nhomalt_nfe_nwe=0;controls_AC_sas=0;controls_AN_sas=15690;controls_AF_sas=0;controls_nhomalt_sas=0;non_neuro_AC_sas_male=0;non_neuro_AN_sas_male=23066;non_neuro_AF_sas_male=0;non_neuro_nhomalt_sas_male=0;non_neuro_AC_asj_male=0;non_neuro_AN_asj_male=3126;non_neuro_AF_asj_male=0;non_neuro_nhomalt_asj_male=0;non_cancer_AC_nfe_bgr=0;non_cancer_AN_nfe_bgr=2522;non_cancer_AF_nfe_bgr=0;non_cancer_nhomalt_nfe_bgr=0;controls_AC_oth=0;controls_AN_oth=1914;controls_AF_oth=0;controls_nhomalt_oth=0;non_cancer_AC_eas_female=0;non_cancer_AN_eas_female=8948;non_cancer_AF_eas_female=0;non_cancer_nhomalt_eas_female=0;AC_nfe=0;AN_nfe=113596;AF_nfe=0;nhomalt_nfe=0;non_topmed_AC_female=0;non_topmed_AN_female=111216;non_topmed_AF_female=0;non_topmed_nhomalt_female=0;non_neuro_AC_asj=0;non_neuro_AN_asj=6208;non_neuro_AF_asj=0;non_neuro_nhomalt_asj=0;non_topmed_AC_eas_female=0;non_topmed_AN_eas_female=9328;non_topmed_AF_eas_female=0;non_topmed_nhomalt_eas_female=0;non_neuro_AC_raw=1;non_neuro_AN_raw=208136;non_neuro_AF_raw=4.80455e-06;non_neuro_nhomalt_raw=0;non_topmed_AC_eas=0;non_topmed_AN_eas=18388;non_topmed_AF_eas=0;non_topmed_nhomalt_eas=0;non_topmed_AC_fin_male=1;non_topmed_AN_fin_male=11262;non_topmed_AF_fin_male=8.87942e-05;non_topmed_nhomalt_fin_male=0;non_cancer_AC_asj_male=0;non_cancer_AN_asj_male=4974;non_cancer_AF_asj_male=0;non_cancer_nhomalt_asj_male=0;AC_fin=1;AN_fin=21626;AF_fin=4.62406e-05;nhomalt_fin=0;AC_nfe_male=0;AN_nfe_male=63518;AF_nfe_male=0;nhomalt_nfe_male=0;non_topmed_AC_eas_kor=0;non_topmed_AN_eas_kor=3818;non_topmed_AF_eas_kor=0;non_topmed_nhomalt_eas_kor=0;controls_AC_amr_male=0;controls_AN_amr_male=6882;controls_AF_amr_male=0;controls_nhomalt_amr_male=0;non_neuro_AC_eas_oea=0;non_neuro_AN_eas_oea=9448;non_neuro_AF_eas_oea=0;non_neuro_nhomalt_eas_oea=0;AC_sas_female=0;AN_sas_female=7544;AF_sas_female=0;nhomalt_sas_female=0;controls_AC_afr_female=0;controls_AN_afr_female=4238;controls_AF_afr_female=0;controls_nhomalt_afr_female=0;controls_AC_amr=0;controls_AN_amr=17106;controls_AF_amr=0;controls_nhomalt_amr=0;non_topmed_AC_eas_jpn=0;non_topmed_AN_eas_jpn=152;non_topmed_AF_eas_jpn=0;non_topmed_nhomalt_eas_jpn=0;AC_asj_female=0;AN_asj_female=4894;AF_asj_female=0;nhomalt_asj_female=0;non_topmed_AC_nfe_bgr=0;non_topmed_AN_nfe_bgr=2656;non_topmed_AF_nfe_bgr=0;non_topmed_nhomalt_nfe_bgr=0;non_cancer_AC_nfe_est=0;non_cancer_AN_nfe_est=158;non_cancer_AF_nfe_est=0;non_cancer_nhomalt_nfe_est=0;non_neuro_AC_eas=0;non_neuro_AN_eas=13414;non_neuro_AF_eas=0;non_neuro_nhomalt_eas=0;non_cancer_AC_nfe=0;non_cancer_AN_nfe=102586;non_cancer_AF_nfe=0;non_cancer_nhomalt_nfe=0;non_neuro_AC_male=1;non_neuro_AN_male=112422;non_neuro_AF_male=8.89506e-06;non_neuro_nhomalt_male=0;non_neuro_AC_sas_female=0;non_neuro_AN_sas_female=7542;non_neuro_AF_sas_female=0;non_neuro_nhomalt_sas_female=0;AC_asj=0;AN_asj=10072;AF_asj=0;nhomalt_asj=0;controls_AC_nfe_est=0;controls_AN_nfe_est=70;controls_AF_nfe_est=0;controls_nhomalt_nfe_est=0;non_topmed_AC_asj_female=0;non_topmed_AN_asj_female=4848;non_topmed_AF_asj_female=0;non_topmed_nhomalt_asj_female=0;non_cancer_AC_nfe_swe=0;non_cancer_AN_nfe_swe=25280;non_cancer_AF_nfe_swe=0;non_cancer_nhomalt_nfe_swe=0;non_cancer_AC=1;non_cancer_AN=236722;non_cancer_AF=4.22436e-06;non_cancer_nhomalt=0;non_topmed_AC_oth=0;non_topmed_AN_oth=6054;non_topmed_AF_oth=0;non_topmed_nhomalt_oth=0;non_topmed_AC_fin_female=0;non_topmed_AN_fin_female=10362;non_topmed_AF_fin_female=0;non_topmed_nhomalt_fin_female=0;non_cancer_AC_fin_female=0;non_cancer_AN_fin_female=10352;non_cancer_AF_fin_female=0;non_cancer_nhomalt_fin_female=0;AC_oth=0;AN_oth=6130;AF_oth=0;nhomalt_oth=0;non_neuro_AC_nfe_male=0;non_neuro_AN_nfe_male=49696;non_neuro_AF_nfe_male=0;non_neuro_nhomalt_nfe_male=0;controls_AC_female=0;controls_AN_female=51276;controls_AF_female=0;controls_nhomalt_female=0;non_cancer_AC_fin=1;non_cancer_AN_fin=21610;non_cancer_AF_fin=4.62749e-05;non_cancer_nhomalt_fin=0;non_topmed_AC_fin=1;non_topmed_AN_fin=21624;non_topmed_AF_fin=4.62449e-05;non_topmed_nhomalt_fin=0;non_cancer_AC_eas_oea=0;non_cancer_AN_eas_oea=13792;non_cancer_AF_eas_oea=0;non_cancer_nhomalt_eas_oea=0;non_topmed_AC_nfe_female=0;non_topmed_AN_nfe_female=48732;non_topmed_AF_nfe_female=0;non_topmed_nhomalt_nfe_female=0;non_cancer_AC_sas_male=0;non_cancer_AN_sas_male=23032;non_cancer_AF_sas_male=0;non_cancer_nhomalt_sas_male=0;controls_AC_asj_male=0;controls_AN_asj_male=1106;controls_AF_asj_male=0;controls_nhomalt_asj_male=0;non_cancer_AC_raw=1;non_cancer_AN_raw=236958;non_cancer_AF_raw=4.22016e-06;non_cancer_nhomalt_raw=0;non_cancer_AC_eas_male=0;non_cancer_AN_eas_male=8742;non_cancer_AF_eas_male=0;non_cancer_nhomalt_eas_male=0;non_topmed_AC_asj_male=0;non_topmed_AN_asj_male=5142;non_topmed_AF_asj_male=0;non_topmed_nhomalt_asj_male=0;non_neuro_AC_oth=0;non_neuro_AN_oth=4860;non_neuro_AF_oth=0;non_neuro_nhomalt_oth=0;AC_male=1;AN_male=135792;AF_male=7.3642e-06;nhomalt_male=0;controls_AC_fin_female=0;controls_AN_fin_female=6474;controls_AF_fin_female=0;controls_nhomalt_fin_female=0;controls_AC_nfe_bgr=0;controls_AN_nfe_bgr=678;controls_AF_nfe_bgr=0;controls_nhomalt_nfe_bgr=0;controls_AC_asj_female=0;controls_AN_asj_female=1214;controls_AF_asj_female=0;controls_nhomalt_asj_female=0;AC_amr_male=0;AN_amr_male=14310;AF_amr_male=0;nhomalt_amr_male=0;AC_amr_female=0;AN_amr_female=20260;AF_amr_female=0;nhomalt_amr_female=0;non_topmed_AC_sas_male=0;non_topmed_AN_sas_male=23072;non_topmed_AF_sas_male=0;non_topmed_nhomalt_sas_male=0;AC_oth_male=0;AN_oth_male=3202;AF_oth_male=0;nhomalt_oth_male=0;non_cancer_AC_sas=0;non_cancer_AN_sas=30526;non_cancer_AF_sas=0;non_cancer_nhomalt_sas=0;non_neuro_AC_nfe_seu=0;non_neuro_AN_nfe_seu=10916;non_neuro_AF_nfe_seu=0;non_neuro_nhomalt_nfe_seu=0;non_cancer_AC_eas_kor=0;non_cancer_AN_eas_kor=3774;non_cancer_AF_eas_kor=0;non_cancer_nhomalt_eas_kor=0;non_topmed_AC_afr_female=0;non_topmed_AN_afr_female=7340;non_topmed_AF_afr_female=0;non_topmed_nhomalt_afr_female=0;controls_AC_sas_male=0;controls_AN_sas_male=11476;controls_AF_sas_male=0;controls_nhomalt_sas_male=0;non_topmed_AC_sas_female=0;non_topmed_AN_sas_female=7544;non_topmed_AF_sas_female=0;non_topmed_nhomalt_sas_female=0;non_topmed_AC_afr=0;non_topmed_AN_afr=12026;non_topmed_AF_afr=0;non_topmed_nhomalt_afr=0;controls_AC=0;controls_AN=109370;controls_AF=0;controls_nhomalt=0;non_neuro_AC_oth_female=0;non_neuro_AN_oth_female=2390;non_neuro_AF_oth_female=0;non_neuro_nhomalt_oth_female=0;non_topmed_faf95_amr=0;non_topmed_faf99_amr=0;faf95_afr=0;faf99_afr=0;faf95_sas=0;faf99_sas=0;controls_faf95_afr=0;controls_faf99_afr=0;faf95_amr=0;faf99_amr=0;non_neuro_faf95_sas=0;non_neuro_faf99_sas=0;faf95_eas=0;faf99_eas=0;faf95=0;faf99=0;non_neuro_faf95_afr=0;non_neuro_faf99_afr=0;non_cancer_faf95_eas=0;non_cancer_faf99_eas=0;non_neuro_faf95_amr=0;non_neuro_faf99_amr=0;non_topmed_faf95_sas=0;non_topmed_faf99_sas=0;controls_faf95_nfe=0;controls_faf99_nfe=0;non_cancer_faf95_afr=0;non_cancer_faf99_afr=0;non_cancer_faf95_amr=0;non_cancer_faf99_amr=0;non_topmed_faf95=0;non_topmed_faf99=0;non_neuro_faf95_nfe=0;non_neuro_faf99_nfe=0;non_neuro_faf95=0;non_neuro_faf99=0;non_topmed_faf95_nfe=0;non_topmed_faf99_nfe=0;controls_faf95_eas=0;controls_faf99_eas=0;controls_faf95_sas=0;controls_faf99_sas=0;faf95_nfe=0;faf99_nfe=0;non_topmed_faf95_eas=0;non_topmed_faf99_eas=0;controls_faf95_amr=0;controls_faf99_amr=0;non_neuro_faf95_eas=0;non_neuro_faf99_eas=0;non_cancer_faf95_nfe=0;non_cancer_faf99_nfe=0;non_cancer_faf95=0;non_cancer_faf99=0;non_cancer_faf95_sas=0;non_cancer_faf99_sas=0;non_topmed_faf95_afr=0;non_topmed_faf99_afr=0;controls_faf95=0;controls_faf99=0;age_hist_het_bin_freq=0|0|0|0|0|0|1|0|0|0;age_hist_het_n_smaller=0;age_hist_het_n_larger=0;age_hist_hom_bin_freq=0|0|0|0|0|0|0|0|0|0;age_hist_hom_n_smaller=0;age_hist_hom_n_larger=0;vep=ACTCGAATGACA|inframe_insertion|MODERATE|MTOR|ENSG00000198793|Transcript|ENST00000361445|protein_coding|19/58||ENST00000361445.4:c.2996_2997insTGTCATTCGAGT|ENSP00000354558.4:p.Val1000_Val1003dup|3073-3074|2996-2997|999|N/NVIRV|aac/aaTGTCATTCGAGTc|rs767390051|1||-1||insertion|1|HGNC|3942|YES|||CCDS127.1|ENSP00000354558|P42345|Q96QW8&B1AKQ2&B1AKP8|UPI000012ABD3|1|||hmmpanther:PTHR11139&hmmpanther:PTHR11139:SF63&Pfam_domain:PF11865&Gene3D:1.25.10.10&Superfamily_domains:SSF48371||||||||||||||||||||||||||||||,ACTCGAATGACA|downstream_gene_variant|MODIFIER|RNU6-291P|ENSG00000207451|Transcript|ENST00000384720|snRNA||||||||||rs767390051|1|2341|1||insertion|1|HGNC|47254|YES|||||||||||||||||||||||||||||||||||||||||,ACTCGAATGACA|upstream_gene_variant|MODIFIER|RPL39P6|ENSG00000238173|Transcript|ENST00000448289|processed_pseudogene||||||||||rs767390051|1|4261|1||insertion|1|HGNC|35803|YES|||||||||||||||||||||||||||||||||||||||||
1   13695794    rs769507157 T   A   745.15  PASS    AC=1;AN=158100;AF=6.32511e-06;rf_tp_probability=0.393721;FS=1.55;InbreedingCoeff=-0.017;MQ=26.76;MQRankSum=-1.21;QD=8.01;ReadPosRankSum=0.62;SOR=0.536;BaseQRankSum=1.68;ClippingRankSum=0.416;DP=7201255;VQSLOD=2.46;VQSR_culprit=MQ;segdup;rf_negative_label;rf_label=FP;rf_train;variant_type=snv;allele_type=snv;n_alt_alleles=1;pab_max=0.716301;gq_hist_alt_bin_freq=0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|0|1;gq_hist_all_bin_freq=4445|13331|7265|12346|10311|4676|8318|7022|2948|4654|3431|1342|3162|364|1183|402|982|105|722|36910;dp_hist_alt_bin_freq=0|0|0|0|0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0;dp_hist_alt_n_larger=0;dp_hist_all_bin_freq=19725|25905|19803|11988|6728|2844|1734|2274|1547|1166|1453|1914|2484|2866|3012|2824|2589|2215|1832|1820;dp_hist_all_n_larger=9025;ab_hist_alt_bin_freq=0|0|0|0|0|0|0|0|0|1|0|0|0|0|0|0|0|0|0|0;AC_nfe_seu=0;AN_nfe_seu=7616;AF_nfe_seu=0;nhomalt_nfe_seu=0;controls_AC_afr_male=0;controls_AN_afr_male=2262;controls_AF_afr_male=0;controls_nhomalt_afr_male=0;non_neuro_AC_eas_kor=0;non_neuro_AN_eas_kor=3702;non_neuro_AF_eas_kor=0;non_neuro_nhomalt_eas_kor=0;non_topmed_AC_amr=0;non_topmed_AN_amr=18444;non_topmed_AF_amr=0;non_topmed_nhomalt_amr=0;non_cancer_AC_asj_female=0;non_cancer_AN_asj_female=1684;non_cancer_AF_asj_female=0;non_cancer_nhomalt_asj_female=0;AC_raw=1;AN_raw=247838;AF_raw=4.03489e-06;nhomalt_raw=0;AC_fin_female=0;AN_fin_female=7530;AF_fin_female=0;nhomalt_fin_female=0;non_cancer_AC_oth_female=1;non_cancer_AN_oth_female=1606;non_cancer_AF_oth_female=0.000622665;non_cancer_nhomalt_oth_female=0;AC_nfe_bgr=0;AN_nfe_bgr=2204;AF_nfe_bgr=0;nhomalt_nfe_bgr=0;non_neuro_AC_asj_female=0;non_neuro_AN_asj_female=1228;non_neuro_AF_asj_female=0;non_neuro_nhomalt_asj_female=0;AC_sas_male=0;AN_sas_male=9104;AF_sas_male=0;nhomalt_sas_male=0;non_neuro_AC_afr_male=0;non_neuro_AN_afr_male=4646;non_neuro_AF_afr_male=0;non_neuro_nhomalt_afr_male=0;AC_afr_male=0;AN_afr_male=4666;AF_afr_male=0;nhomalt_afr_male=0;AC_afr=0;AN_afr=11332;AF_afr=0;nhomalt_afr=0;controls_AC_nfe_swe=0;controls_AN_nfe_swe=10392;controls_AF_nfe_swe=0;controls_nhomalt_nfe_swe=0;non_neuro_AC_afr_female=0;non_neuro_AN_afr_female=6650;non_neuro_AF_afr_female=0;non_neuro_nhomalt_afr_female=0;non_topmed_AC_amr_female=0;non_topmed_AN_amr_female=10504;non_topmed_AF_amr_female=0;non_topmed_nhomalt_amr_female=0;non_cancer_AC_female=1;non_cancer_AN_female=67364;non_cancer_AF_female=1.48447e-05;non_cancer_nhomalt_female=0;non_cancer_AC_nfe_onf=0;non_cancer_AN_nfe_onf=13236;non_cancer_AF_nfe_onf=0;non_cancer_nhomalt_nfe_onf=0;non_cancer_AC_male=0;non_cancer_AN_male=78698;non_cancer_AF_male=0;non_cancer_nhomalt_male=0;non_topmed_AC_oth_female=1;non_topmed_AN_oth_female=1772;non_topmed_AF_oth_female=0.000564334;non_topmed_nhomalt_oth_female=0;AC_eas_female=0;AN_eas_female=7212;AF_eas_female=0;nhomalt_eas_female=0;non_cancer_AC_sas_female=0;non_cancer_AN_sas_female=4140;non_cancer_AF_sas_female=0;non_cancer_nhomalt_sas_female=0;AC_afr_female=0;AN_afr_female=6666;AF_afr_female=0;nhomalt_afr_female=0;AC_sas=0;AN_sas=13286;AF_sas=0;nhomalt_sas=0;non_neuro_AC_female=1;non_neuro_AN_female=60014;non_neuro_AF_female=1.66628e-05;non_neuro_nhomalt_female=0;controls_AC_afr=0;controls_AN_afr=5406;controls_AF_afr=0;controls_nhomalt_afr=0;non_neuro_AC_eas_jpn=0;non_neuro_AN_eas_jpn=114;non_neuro_AF_eas_jpn=0;non_neuro_nhomalt_eas_jpn=0;AC_nfe_onf=0;AN_nfe_onf=18468;AF_nfe_onf=0;nhomalt_nfe_onf=0;non_cancer_AC_amr_male=0;non_cancer_AN_amr_male=7876;non_cancer_AF_amr_male=0;non_cancer_nhomalt_amr_male=0;controls_AC_fin_male=0;controls_AN_fin_male=5680;controls_AF_fin_male=0;controls_nhomalt_fin_male=0;non_neuro_AC_nfe_nwe=0;non_neuro_AN_nfe_nwe=22156;non_neuro_AF_nfe_nwe=0;non_neuro_nhomalt_nfe_nwe=0;AC_fin_male=0;AN_fin_male=8166;AF_fin_male=0;nhomalt_fin_male=0;AC_nfe_female=0;AN_nfe_female=34222;AF_nfe_female=0;nhomalt_nfe_female=0;AC_amr=0;AN_amr=18518;AF_amr=0;nhomalt_amr=0;non_topmed_AC_nfe_male=0;non_topmed_AN_nfe_male=42742;non_topmed_AF_nfe_male=0;non_topmed_nhomalt_nfe_male=0;non_neuro_AC_sas=0;non_neuro_AN_sas=13280;non_neuro_AF_sas=0;non_neuro_nhomalt_sas=0;non_cancer_AC_fin_male=0;non_cancer_AN_fin_male=8164;non_cancer_AF_fin_male=0;non_cancer_nhomalt_fin_male=0;non_cancer_AC_nfe_seu=0;non_cancer_AN_nfe_seu=6882;non_cancer_AF_nfe_seu=0;non_cancer_nhomalt_nfe_seu=0;AC_eas=0;AN_eas=14210;AF_eas=0;nhomalt_eas=0;nhomalt=0;non_neuro_AC_nfe_female=0;non_neuro_AN_nfe_female=25372;non_neuro_AF_nfe_female=0;non_neuro_nhomalt_nfe_female=0;non_neuro_AC_afr=0;non_neuro_AN_afr=11296;non_neuro_AF_afr=0;non_neuro_nhomalt_afr=0;controls_AC_raw=1;controls_AN_raw=108204;controls_AF_raw=9.2418e-06;controls_nhomalt_raw=0;non_cancer_AC_eas=0;non_cancer_AN_eas=13636;non_cancer_AF_eas=0;non_cancer_nhomalt_eas=0;non_cancer_AC_amr_female=0;non_cancer_AN_amr_female=10404;non_cancer_AF_amr_female=0;non_cancer_nhomalt_amr_female=0;non_neuro_AC_nfe_swe=0;non_neuro_AN_nfe_swe=11088;non_neuro_AF_nfe_swe=0;non_neuro_nhomalt_nfe_swe=0;controls_AC_male=0;controls_AN_male=35994;controls_AF_male=0;controls_nhomalt_male=0;non_topmed_AC_male=0;non_topmed_AN_male=82572;non_topmed_AF_male=0;non_topmed_nhomalt_male=0;controls_AC_eas_jpn=0;controls_AN_eas_jpn=92;controls_AF_eas_jpn=0;controls_nhomalt_eas_jpn=0;controls_AC_nfe_female=0;controls_AN_nfe_female=12370;controls_AF_nfe_female=0;controls_nhomalt_nfe_female=0;non_neuro_AC_amr=0;non_neuro_AN_amr=15152;non_neuro_AF_amr=0;non_neuro_nhomalt_amr=0;non_neuro_AC_eas_female=0;non_neuro_AN_eas_female=6252;non_neuro_AF_eas_female=0;non_neuro_nhomalt_eas_female=0;AC_asj_male=0;AN_asj_male=1776;AF_asj_male=0;nhomalt_asj_male=0;controls_AC_nfe_male=0;controls_AN_nfe_male=15074;controls_AF_nfe_male=0;controls_nhomalt_nfe_male=0;non_neuro_AC_fin=0;non_neuro_AN_fin=12980;non_neuro_AF_fin=0;non_neuro_nhomalt_fin=0;non_topmed_AC_sas=0;non_topmed_AN_sas=13286;non_topmed_AF_sas=0;non_topmed_nhomalt_sas=0;non_cancer_AC_nfe_female=0;non_cancer_AN_nfe_female=29176;non_cancer_AF_nfe_female=0;non_cancer_nhomalt_nfe_female=0;AC_oth_female=1;AN_oth_female=1800;AF_oth_female=0.000555556;nhomalt_oth_female=0;non_cancer_AC_asj=0;non_cancer_AN_asj=3288;non_cancer_AF_asj=0;non_cancer_nhomalt_asj=0;AC_nfe_swe=0;AN_nfe_swe=20582;AF_nfe_swe=0;nhomalt_nfe_swe=0;controls_AC_nfe=0;controls_AN_nfe=27444;controls_AF_nfe=0;controls_nhomalt_nfe=0;controls_AC_oth_female=1;controls_AN_oth_female=642;controls_AF_oth_female=0.00155763;controls_nhomalt_oth_female=0;controls_AC_asj=0;controls_AN_asj=984;controls_AF_asj=0;controls_nhomalt_asj=0;non_neuro_AC_amr_male=0;non_neuro_AN_amr_male=6340;non_neuro_AF_amr_male=0;non_neuro_nhomalt_amr_male=0;controls_AC_nfe_nwe=0;controls_AN_nfe_nwe=8332;controls_AF_nfe_nwe=0;controls_nhomalt_nfe_nwe=0;AC_nfe_nwe=0;AN_nfe_nwe=28490;AF_nfe_nwe=0;nhomalt_nfe_nwe=0;controls_AC_nfe_seu=0;controls_AN_nfe_seu=3236;controls_AF_nfe_seu=0;controls_nhomalt_nfe_seu=0;controls_AC_sas_female=0;controls_AN_sas_female=2208;controls_AF_sas_female=0;controls_nhomalt_sas_female=0;non_neuro_AC_amr_female=0;non_neuro_AN_amr_female=8812;non_neuro_AF_amr_female=0;non_neuro_nhomalt_amr_female=0;non_cancer_AC_eas_jpn=0;non_cancer_AN_eas_jpn=94;non_cancer_AF_eas_jpn=0;non_cancer_nhomalt_eas_jpn=0;non_neuro_AC_nfe_onf=0;non_neuro_AN_nfe_onf=15792;non_neuro_AF_nfe_onf=0;non_neuro_nhomalt_nfe_onf=0;non_topmed_AC_eas_male=0;non_topmed_AN_eas_male=6996;non_topmed_AF_eas_male=0;non_topmed_nhomalt_eas_male=0;AC_eas_jpn=0;AN_eas_jpn=116;AF_eas_jpn=0;nhomalt_eas_jpn=0;non_cancer_AC_afr_male=0;non_cancer_AN_afr_male=4282;non_cancer_AF_afr_male=0;non_cancer_nhomalt_afr_male=0;non_cancer_AC_afr=0;non_cancer_AN_afr=10222;non_cancer_AF_afr=0;non_cancer_nhomalt_afr=0;controls_AC_amr_female=0;controls_AN_amr_female=5432;controls_AF_amr_female=0;controls_nhomalt_amr_female=0;non_neuro_AC_fin_male=0;non_neuro_AN_fin_male=6898;non_neuro_AF_fin_male=0;non_neuro_nhomalt_fin_male=0;AC_female=1;AN_female=74116;AF_female=1.34924e-05;nhomalt_female=0;non_neuro_AC_nfe_bgr=0;non_neuro_AN_nfe_bgr=204;non_neuro_AF_nfe_bgr=0;non_neuro_nhomalt_nfe_bgr=0;non_neuro_AC_oth_male=0;non_neuro_AN_oth_male=1432;non_neuro_AF_oth_male=0;non_neuro_nhomalt_oth_male=0;non_topmed_AC_nfe_est=0;non_topmed_AN_nfe_est=164;non_topmed_AF_nfe_est=0;non_topmed_nhomalt_nfe_est=0;non_topmed_AC_nfe_nwe=0;non_topmed_AN_nfe_nwe=27708;non_topmed_AF_nfe_nwe=0;non_topmed_nhomalt_nfe_nwe=0;non_topmed_AC_amr_male=0;non_topmed_AN_amr_male=7940;non_topmed_AF_amr_male=0;non_topmed_nhomalt_amr_male=0;non_cancer_AC_amr=0;non_cancer_AN_amr=18280;non_cancer_AF_amr=0;non_cancer_nhomalt_amr=0;non_topmed_AC_nfe_swe=0;non_topmed_AN_nfe_swe=20560;non_topmed_AF_nfe_swe=0;non_topmed_nhomalt_nfe_swe=0;non_topmed_AC_nfe_onf=0;non_topmed_AN_nfe_onf=18032;non_topmed_AF_nfe_onf=0;non_topmed_nhomalt_nfe_onf=0;controls_AC_eas_kor=0;controls_AN_eas_kor=1836;controls_AF_eas_kor=0;controls_nhomalt_eas_kor=0;non_topmed_AC_eas_oea=0;non_topmed_AN_eas_oea=10388;non_topmed_AF_eas_oea=0;non_topmed_nhomalt_eas_oea=0;controls_AC_eas_male=0;controls_AN_eas_male=3560;controls_AF_eas_male=0;controls_nhomalt_eas_male=0;controls_AC_oth_male=0;controls_AN_oth_male=580;controls_AF_oth_male=0;controls_nhomalt_oth_male=0;non_topmed_AC=1;non_topmed_AN=154576;non_topmed_AF=6.46931e-06;non_topmed_nhomalt=0;controls_AC_fin=0;controls_AN_fin=11350;controls_AF_fin=0;controls_nhomalt_fin=0;AC_eas_kor=0;AN_eas_kor=3704;AF_eas_kor=0;nhomalt_eas_kor=0;non_neuro_AC_nfe=0;non_neuro_AN_nfe=56598;non_neuro_AF_nfe=0;non_neuro_nhomalt_nfe=0;non_neuro_AC_fin_female=0;non_neuro_AN_fin_female=6082;non_neuro_AF_fin_female=0;non_neuro_nhomalt_fin_female=0;non_cancer_AC_nfe_male=0;non_cancer_AN_nfe_male=39162;non_cancer_AF_nfe_male=0;non_cancer_nhomalt_nfe_male=0;controls_AC_eas_oea=0;controls_AN_eas_oea=5684;controls_AF_eas_oea=0;controls_nhomalt_eas_oea=0;non_topmed_AC_nfe_seu=0;non_topmed_AN_nfe_seu=7578;non_topmed_AF_nfe_seu=0;non_topmed_nhomalt_nfe_seu=0;controls_AC_eas_female=0;controls_AN_eas_female=4052;controls_AF_eas_female=0;controls_nhomalt_eas_female=0;non_topmed_AC_asj=0;non_topmed_AN_asj=3700;non_topmed_AF_asj=0;non_topmed_nhomalt_asj=0;controls_AC_nfe_onf=0;controls_AN_nfe_onf=4932;controls_AF_nfe_onf=0;controls_nhomalt_nfe_onf=0;non_neuro_AC=1;non_neuro_AN=126866;non_neuro_AF=7.88233e-06;non_neuro_nhomalt=0;AC_eas_oea=0;AN_eas_oea=10390;AF_eas_oea=0;nhomalt_eas_oea=0;non_topmed_AC_nfe=0;non_topmed_AN_nfe=76244;non_topmed_AF_nfe=0;non_topmed_nhomalt_nfe=0;non_cancer_AC_oth=1;non_cancer_AN_oth=3400;non_cancer_AF_oth=0.000294118;non_cancer_nhomalt_oth=0;non_topmed_AC_raw=1;non_topmed_AN_raw=241442;non_topmed_AF_raw=4.14178e-06;non_topmed_nhomalt_raw=0;non_neuro_AC_nfe_est=0;non_neuro_AN_nfe_est=144;non_neuro_AF_nfe_est=0;non_neuro_nhomalt_nfe_est=0;non_topmed_AC_oth_male=0;non_topmed_AN_oth_male=1976;non_topmed_AF_oth_male=0;non_topmed_nhomalt_oth_male=0;non_cancer_AC_oth_male=0;non_cancer_AN_oth_male=1794;non_cancer_AF_oth_male=0;non_cancer_nhomalt_oth_male=0;AC_nfe_est=0;AN_nfe_est=168;AF_nfe_est=0;nhomalt_nfe_est=0;non_cancer_AC_afr_female=0;non_cancer_AN_afr_female=5940;non_cancer_AF_afr_female=0;non_cancer_nhomalt_afr_female=0;non_topmed_AC_afr_male=0;non_topmed_AN_afr_male=3886;non_topmed_AF_afr_male=0;non_topmed_nhomalt_afr_male=0;AC_eas_male=0;AN_eas_male=6998;AF_eas_male=0;nhomalt_eas_male=0;controls_AC_eas=0;controls_AN_eas=7612;controls_AF_eas=0;controls_nhomalt_eas=0;non_neuro_AC_eas_male=0;non_neuro_AN_eas_male=6042;non_neuro_AF_eas_male=0;non_neuro_nhomalt_eas_male=0;non_cancer_AC_nfe_nwe=0;non_cancer_AN_nfe_nwe=26162;non_cancer_AF_nfe_nwe=0;non_cancer_nhomalt_nfe_nwe=0;controls_AC_sas=0;controls_AN_sas=6746;controls_AF_sas=0;controls_nhomalt_sas=0;non_neuro_AC_sas_male=0;non_neuro_AN_sas_male=9098;non_neuro_AF_sas_male=0;non_neuro_nhomalt_sas_male=0;non_neuro_AC_asj_male=0;non_neuro_AN_asj_male=1170;non_neuro_AF_asj_male=0;non_neuro_nhomalt_asj_male=0;non_cancer_AC_nfe_bgr=0;non_cancer_AN_nfe_bgr=2088;non_cancer_AF_nfe_bgr=0;non_cancer_nhomalt_nfe_bgr=0;controls_AC_oth=1;controls_AN_oth=1222;controls_AF_oth=0.000818331;controls_nhomalt_oth=0;non_cancer_AC_eas_female=0;non_cancer_AN_eas_female=6894;non_cancer_AF_eas_female=0;non_cancer_nhomalt_eas_female=0;AC_nfe=0;AN_nfe=77528;AF_nfe=0;nhomalt_nfe=0;non_topmed_AC_female=1;non_topmed_AN_female=72004;non_topmed_AF_female=1.38881e-05;non_topmed_nhomalt_female=0;non_neuro_AC_asj=0;non_neuro_AN_asj=2398;non_neuro_AF_asj=0;non_neuro_nhomalt_asj=0;non_topmed_AC_eas_female=0;non_topmed_AN_eas_female=7212;non_topmed_AF_eas_female=0;non_topmed_nhomalt_eas_female=0;non_neuro_AC_raw=1;non_neuro_AN_raw=205168;non_neuro_AF_raw=4.87405e-06;non_neuro_nhomalt_raw=0;non_topmed_AC_eas=0;non_topmed_AN_eas=14208;non_topmed_AF_eas=0;non_topmed_nhomalt_eas=0;non_topmed_AC_fin_male=0;non_topmed_AN_fin_male=8166;non_topmed_AF_fin_male=0;non_topmed_nhomalt_fin_male=0;non_cancer_AC_asj_male=0;non_cancer_AN_asj_male=1604;non_cancer_AF_asj_male=0;non_cancer_nhomalt_asj_male=0;AC_fin=0;AN_fin=15696;AF_fin=0;nhomalt_fin=0;AC_nfe_male=0;AN_nfe_male=43306;AF_nfe_male=0;nhomalt_nfe_male=0;non_topmed_AC_eas_kor=0;non_topmed_AN_eas_kor=3704;non_topmed_AF_eas_kor=0;non_topmed_nhomalt_eas_kor=0;controls_AC_amr_male=0;controls_AN_amr_male=3836;controls_AF_amr_male=0;controls_nhomalt_amr_male=0;non_neuro_AC_eas_oea=0;non_neuro_AN_eas_oea=8478;non_neuro_AF_eas_oea=0;non_neuro_nhomalt_eas_oea=0;AC_sas_female=0;AN_sas_female=4182;AF_sas_female=0;nhomalt_sas_female=0;controls_AC_afr_female=0;controls_AN_afr_female=3144;controls_AF_afr_female=0;controls_nhomalt_afr_female=0;controls_AC_amr=0;controls_AN_amr=9268;controls_AF_amr=0;controls_nhomalt_amr=0;non_topmed_AC_eas_jpn=0;non_topmed_AN_eas_jpn=116;non_topmed_AF_eas_jpn=0;non_topmed_nhomalt_eas_jpn=0;AC_asj_female=0;AN_asj_female=1956;AF_asj_female=0;nhomalt_asj_female=0;non_topmed_AC_nfe_bgr=0;non_topmed_AN_nfe_bgr=2202;non_topmed_AF_nfe_bgr=0;non_topmed_nhomalt_nfe_bgr=0;non_cancer_AC_nfe_est=0;non_cancer_AN_nfe_est=90;non_cancer_AF_nfe_est=0;non_cancer_nhomalt_nfe_est=0;non_neuro_AC_eas=0;non_neuro_AN_eas=12294;non_neuro_AF_eas=0;non_neuro_nhomalt_eas=0;non_cancer_AC_nfe=0;non_cancer_AN_nfe=68338;non_cancer_AF_nfe=0;non_cancer_nhomalt_nfe=0;non_neuro_AC_male=0;non_neuro_AN_male=66852;non_neuro_AF_male=0;non_neuro_nhomalt_male=0;non_neuro_AC_sas_female=0;non_neuro_AN_sas_female=4182;non_neuro_AF_sas_female=0;non_neuro_nhomalt_sas_female=0;AC_asj=0;AN_asj=3732;AF_asj=0;nhomalt_asj=0;controls_AC_nfe_est=0;controls_AN_nfe_est=32;controls_AF_nfe_est=0;controls_nhomalt_nfe_est=0;non_topmed_AC_asj_female=0;non_topmed_AN_asj_female=1938;non_topmed_AF_asj_female=0;non_topmed_nhomalt_asj_female=0;non_cancer_AC_nfe_swe=0;non_cancer_AN_nfe_swe=19880;non_cancer_AF_nfe_swe=0;non_cancer_nhomalt_nfe_swe=0;non_cancer_AC=1;non_cancer_AN=146062;non_cancer_AF=6.84641e-06;non_cancer_nhomalt=0;non_topmed_AC_oth=1;non_topmed_AN_oth=3748;non_topmed_AF_oth=0.000266809;non_topmed_nhomalt_oth=0;non_topmed_AC_fin_female=0;non_topmed_AN_fin_female=7528;non_topmed_AF_fin_female=0;non_topmed_nhomalt_fin_female=0;non_cancer_AC_fin_female=0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|1|HGNC|24908|YES||||ENSP00000446004||F5H544|UPI0000237231|||benign(0.083)|Gene3D:3.80.10.10&PIRSF_domain:PIRSF038286&hmmpanther:PTHR14224&hmmpanther:PTHR14224:SF5&Superfamily_domains:SSF52047|||A:0||||||||A:0|A:8.384e-06|A:0|A:1.313e-05|A:0|A:0|A:0|A:0.001859||||||||||||
1   16374997    rs1274302758    A   T   2487.77 PASS    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336;non_topmed_AF_male=7.49985e-06;non_topmed_nhomalt_male=0;controls_AC_eas_jpn=0;controls_AN_eas_jpn=114;controls_AF_eas_jpn=0;controls_nhomalt_eas_jpn=0;controls_AC_nfe_female=0;controls_AN_nfe_female=19126;controls_AF_nfe_female=0;controls_nhomalt_nfe_female=0;non_neuro_AC_amr=0;non_neuro_AN_amr=30516;non_neuro_AF_amr=0;non_neuro_nhomalt_amr=0;non_neuro_AC_eas_female=0;non_neuro_AN_eas_female=6838;non_neuro_AF_eas_female=0;non_neuro_nhomalt_eas_female=0;AC_asj_male=0;AN_asj_male=5176;AF_asj_male=0;nhomalt_asj_male=0;controls_AC_nfe_male=0;controls_AN_nfe_male=23606;controls_AF_nfe_male=0;controls_nhomalt_nfe_male=0;non_neuro_AC_fin=1;non_neuro_AN_fin=16734;non_neuro_AF_fin=5.97586e-05;non_neuro_nhomalt_fin=0;non_topmed_AC_sas=0;non_topmed_AN_sas=30616;non_topmed_AF_sas=0;non_topmed_nhomalt_sas=0;non_cancer_AC_nfe_female=0;non_cancer_AN_nfe_female=44142;non_cancer_AF_nfe_female=0;non_cancer_nhomalt_nfe_female=0;AC_oth_female=0;AN_oth_female=2914;AF_oth_female=0;nhomalt_oth_female=0;non_cancer_AC_asj=0;non_cancer_AN_asj=9564;non_cancer_AF_asj=0;non_cancer_nhomalt_asj=0;AC_nfe_swe=0;AN_nfe_swe=26116;AF_nfe_swe=0;nhomalt_nfe_swe=0;controls_AC_nfe=0;controls_AN_nfe=42732;controls_AF_nfe=0;controls_nhomalt_nfe=0;controls_AC_oth_female=0;controls_AN_oth_female=984;controls_AF_oth_female=0;controls_nhomalt_oth_female=0;controls_AC_asj=0;controls_AN_asj=2320;controls_AF_asj=0;controls_nhomalt_asj=0;non_neuro_AC_amr_male=0;non_neuro_AN_amr_male=12256;non_neuro_AF_amr_male=0;non_neuro_nhomalt_amr_male=0;controls_AC_nfe_nwe=0;controls_AN_nfe_nwe=14446;controls_AF_nfe_nwe=0;controls_nhomalt_nfe_nwe=0;AC_nfe_nwe=0;AN_nfe_nwe=41996;AF_nfe_nwe=0;nhomalt_nfe_nwe=0;controls_AC_nfe_seu=0;controls_AN_nfe_seu=4752;controls_AF_nfe_seu=0;controls_nhomalt_nfe_seu=0;controls_AC_sas_female=0;controls_AN_sas_female=4214;controls_AF_sas_female=0;controls_nhomalt_sas_female=0;non_neuro_AC_amr_female=0;non_neuro_AN_amr_female=18260;non_neuro_AF_amr_female=0;non_neuro_nhomalt_amr_female=0;non_cancer_AC_eas_jpn=0;non_cancer_AN_eas_jpn=124;non_cancer_AF_eas_jpn=0;non_cancer_nhomalt_eas_jpn=0;non_neuro_AC_nfe_onf=0;non_neuro_AN_nfe_onf=27728;non_neuro_AF_nfe_onf=0;non_neuro_nhomalt_nfe_onf=0;non_topmed_AC_eas_male=0;non_topmed_AN_eas_male=9060;non_topmed_AF_eas_male=0;non_topmed_nhomalt_eas_male=0;AC_eas_jpn=0;AN_eas_jpn=152;AF_eas_jpn=0;nhomalt_eas_jpn=0;non_cancer_AC_afr_male=0;non_cancer_AN_afr_male=5662;non_cancer_AF_afr_male=0;non_cancer_nhomalt_afr_male=0;non_cancer_AC_afr=0;non_cancer_AN_afr=14860;non_cancer_AF_afr=0;non_cancer_nhomalt_afr=0;controls_AC_amr_female=0;controls_AN_amr_female=10224;controls_AF_amr_female=0;controls_nhomalt_amr_female=0;non_neuro_AC_fin_male=1;non_neuro_AN_fin_male=9084;non_neuro_AF_fin_male=0.000110084;non_neuro_nhomalt_fin_male=0;AC_female=0;AN_female=115258;AF_female=0;nhomalt_female=0;non_neuro_AC_nfe_bgr=0;non_neuro_AN_nfe_bgr=452;non_neuro_AF_nfe_bgr=0;non_neuro_nhomalt_nfe_bgr=0;non_neuro_AC_oth_male=0;non_neuro_AN_oth_male=2474;non_neuro_AF_oth_male=0;non_neuro_nhomalt_oth_male=0;non_topmed_AC_nfe_est=0;non_topmed_AN_nfe_est=234;non_topmed_AF_nfe_est=0;non_topmed_nhomalt_nfe_est=0;non_topmed_AC_nfe_nwe=0;non_topmed_AN_nfe_nwe=40890;non_topmed_AF_nfe_nwe=0;non_topmed_nhomalt_nfe_nwe=0;non_topmed_AC_amr_male=0;non_topmed_AN_amr_male=14262;non_topmed_AF_amr_male=0;non_topmed_nhomalt_amr_male=0;non_cancer_AC_amr=0;non_cancer_AN_amr=34252;non_cancer_AF_amr=0;non_cancer_nhomalt_amr=0;non_topmed_AC_nfe_swe=0;non_topmed_AN_nfe_swe=26054;non_topmed_AF_nfe_swe=0;non_topmed_nhomalt_nfe_swe=0;non_topmed_AC_nfe_onf=0;non_topmed_AN_nfe_onf=30036;non_topmed_AF_nfe_onf=0;non_topmed_nhomalt_nfe_onf=0;controls_AC_eas_kor=0;controls_AN_eas_kor=1888;controls_AF_eas_kor=0;controls_nhomalt_eas_kor=0;non_topmed_AC_eas_oea=0;non_topmed_AN_eas_oea=14418;non_topmed_AF_eas_oea=0;non_topmed_nhomalt_eas_oea=0;controls_AC_eas_male=0;controls_AN_eas_male=4258;controls_AF_eas_male=0;controls_nhomalt_eas_male=0;controls_AC_oth_male=0;controls_AN_oth_male=928;controls_AF_oth_male=0;controls_nhomalt_oth_male=0;non_topmed_AC=1;non_topmed_AN=244374;non_topmed_AF=4.09209e-06;non_topmed_nhomalt=0;controls_AC_fin=0;controls_AN_fin=13394;controls_AF_fin=0;controls_nhomalt_fin=0;AC_eas_kor=0;AN_eas_kor=3814;AF_eas_kor=0;nhomalt_eas_kor=0;non_neuro_AC_nfe=0;non_neuro_AN_nfe=89390;non_neuro_AF_nfe=0;non_neuro_nhomalt_nfe=0;non_neuro_AC_fin_female=0;non_neuro_AN_fin_female=7650;non_neuro_AF_fin_female=0;non_neuro_nhomalt_fin_female=0;non_cancer_AC_nfe_male=0;non_cancer_AN_nfe_male=58272;non_cancer_AF_nfe_male=0;non_cancer_nhomalt_nfe_male=0;controls_AC_eas_oea=0;controls_AN_eas_oea=7044;controls_AF_eas_oea=0;controls_nhomalt_eas_oea=0;non_topmed_AC_nfe_seu=0;non_topmed_AN_nfe_seu=11390;non_topmed_AF_nfe_seu=0;non_topmed_nhomalt_nfe_seu=0;controls_AC_eas_female=0;controls_AN_eas_female=4788;controls_AF_eas_female=0;controls_nhomalt_eas_female=0;non_topmed_AC_asj=0;non_topmed_AN_asj=9990;non_topmed_AF_asj=0;non_topmed_nhomalt_asj=0;controls_AC_nfe_onf=0;controls_AN_nfe_onf=9984;controls_AF_nfe_onf=0;controls_nhomalt_nfe_onf=0;non_neuro_AC=1;non_neuro_AN=207882;non_neuro_AF=4.81042e-06;non_neuro_nhomalt=0;AC_eas_oea=0;AN_eas_oea=14422;AF_eas_oea=0;nhomalt_eas_oea=0;non_topmed_AC_nfe=0;non_topmed_AN_nfe=111264;non_topmed_AF_nfe=0;non_topmed_nhomalt_nfe=0;non_cancer_AC_oth=0;non_cancer_AN_oth=5608;non_cancer_AF_oth=0;non_cancer_nhomalt_oth=0;non_topmed_AC_raw=1;non_topmed_AN_raw=244866;non_topmed_AF_raw=4.08387e-06;non_topmed_nhomalt_raw=0;non_neuro_AC_nfe_est=0;non_neuro_AN_nfe_est=212;non_neuro_AF_nfe_est=0;non_neuro_nhomalt_nfe_est=0;non_topmed_AC_oth_male=0;non_topmed_AN_oth_male=3184;non_topmed_AF_oth_male=0;non_topmed_nhomalt_oth_male=0;non_cancer_AC_oth_male=0;non_cancer_AN_oth_male=2936;non_cancer_AF_oth_male=0;non_cancer_nhomalt_oth_male=0;AC_nfe_est=0;AN_nfe_est=238;AF_nfe_est=0;nhomalt_nfe_est=0;non_cancer_AC_afr_female=0;non_cancer_AN_afr_female=9198;non_cancer_AF_afr_female=0;non_cancer_nhomalt_afr_female=0;non_topmed_AC_afr_male=0;non_topmed_AN_afr_male=4672;non_topmed_AF_afr_male=0;non_topmed_nhomalt_afr_male=0;AC_eas_male=0;AN_eas_male=9064;AF_eas_male=0;nhomalt_eas_male=0;controls_AC_eas=0;controls_AN_eas=9046;controls_AF_eas=0;controls_nhomalt_eas=0;non_neuro_AC_eas_male=0;non_neuro_AN_eas_male=6572;non_neuro_AF_eas_male=0;non_neuro_nhomalt_eas_male=0;non_cancer_AC_nfe_nwe=0;non_cancer_AN_nfe_nwe=39296;non_cancer_AF_nfe_nwe=0;non_cancer_nhomalt_nfe_nwe=0;controls_AC_sas=0;controls_AN_sas=15690;controls_AF_sas=0;controls_nhomalt_sas=0;non_neuro_AC_sas_male=0;non_neuro_AN_sas_male=23066;non_neuro_AF_sas_male=0;non_neuro_nhomalt_sas_male=0;non_neuro_AC_asj_male=0;non_neuro_AN_asj_male=3122;non_neuro_AF_asj_male=0;non_neuro_nhomalt_asj_male=0;non_cancer_AC_nfe_bgr=0;non_cancer_AN_nfe_bgr=2524;non_cancer_AF_nfe_bgr=0;non_cancer_nhomalt_nfe_bgr=0;controls_AC_oth=0;controls_AN_oth=1912;controls_AF_oth=0;controls_nhomalt_oth=0;non_cancer_AC_eas_female=0;non_cancer_AN_eas_female=8948;non_cancer_AF_eas_female=0;non_cancer_nhomalt_eas_female=0;AC_nfe=0;AN_nfe=113328;AF_nfe=0;nhomalt_nfe=0;non_topmed_AC_female=0;non_topmed_AN_female=111038;non_topmed_AF_female=0;non_topmed_nhomalt_female=0;non_neuro_AC_asj=0;non_neuro_AN_asj=6200;non_neuro_AF_asj=0;non_neuro_nhomalt_asj=0;non_topmed_AC_eas_female=0;non_topmed_AN_eas_female=9324;non_topmed_AF_eas_female=0;non_topmed_nhomalt_eas_female=0;non_neuro_AC_raw=1;non_neuro_AN_raw=208120;non_neuro_AF_raw=4.80492e-06;non_neuro_nhomalt_raw=0;non_topmed_AC_eas=0;non_topmed_AN_eas=18384;non_topmed_AF_eas=0;non_topmed_nhomalt_eas=0;non_topmed_AC_fin_male=1;non_topmed_AN_fin_male=11272;non_topmed_AF_fin_male=8.87154e-05;non_topmed_nhomalt_fin_male=0;non_cancer_AC_asj_male=0;non_cancer_AN_asj_male=4974;non_cancer_AF_asj_male=0;non_cancer_nhomalt_asj_male=0;AC_fin=1;AN_fin=21642;AF_fin=4.62065e-05;nhomalt_fin=0;AC_nfe_male=0;AN_nfe_male=63410;AF_nfe_male=0;nhomalt_nfe_male=0;non_topmed_AC_eas_kor=0;non_topmed_AN_eas_kor=3814;non_topmed_AF_eas_kor=0;non_topmed_nhomalt_eas_kor=0;controls_AC_amr_male=0;controls_AN_amr_male=6884;controls_AF_amr_male=0;controls_nhomalt_amr_male=0;non_neuro_AC_eas_oea=0;non_neuro_AN_eas_oea=9448;non_neuro_AF_eas_oea=0;non_neuro_nhomalt_eas_oea=0;AC_sas_female=0;AN_sas_female=7544;AF_sas_female=0;nhomalt_sas_female=0;controls_AC_afr_female=0;controls_AN_afr_female=4236;controls_AF_afr_female=0;controls_nhomalt_afr_female=0;controls_AC_amr=0;controls_AN_amr=17108;controls_AF_amr=0;controls_nhomalt_amr=0;non_topmed_AC_eas_jpn=0;non_topmed_AN_eas_jpn=152;non_topmed_AF_eas_jpn=0;non_topmed_nhomalt_eas_jpn=0;AC_asj_female=0;AN_asj_female=4892;AF_asj_female=0;nhomalt_asj_female=0;non_topmed_AC_nfe_bgr=0;non_topmed_AN_nfe_bgr=2660;non_topmed_AF_nfe_bgr=0;non_topmed_nhomalt_nfe_bgr=0;non_cancer_AC_nfe_est=0;non_cancer_AN_nfe_est=156;non_cancer_AF_nfe_est=0;non_cancer_nhomalt_nfe_est=0;non_neuro_AC_eas=0;non_neuro_AN_eas=13410;non_neuro_AF_eas=0;non_neuro_nhomalt_eas=0;non_cancer_AC_nfe=0;non_cancer_AN_nfe=102414;non_cancer_AF_nfe=0;non_cancer_nhomalt_nfe=0;non_neuro_AC_male=1;non_neuro_AN_male=112412;non_neuro_AF_male=8.89585e-06;non_neuro_nhomalt_male=0;non_neuro_AC_sas_female=0;non_neuro_AN_sas_female=7542;non_neuro_AF_sas_female=0;non_neuro_nhomalt_sas_female=0;AC_asj=0;AN_asj=10068;AF_asj=0;nhomalt_asj=0;controls_AC_nfe_est=0;controls_AN_nfe_est=68;controls_AF_nfe_est=0;controls_nhomalt_nfe_est=0;non_topmed_AC_asj_female=0;non_topmed_AN_asj_female=4848;non_topmed_AF_asj_female=0;non_topmed_nhomalt_asj_female=0;non_cancer_AC_nfe_swe=0;non_cancer_AN_nfe_swe=25286;non_cancer_AF_nfe_swe=0;non_cancer_nhomalt_nfe_swe=0;non_cancer_AC=1;non_cancer_AN=236542;non_cancer_AF=4.22758e-06;non_cancer_nhomalt=0;non_topmed_AC_oth=0;non_topmed_AN_oth=6048;non_topmed_AF_oth=0;non_topmed_nhomalt_oth=0;non_topmed_AC_fin_female=0;non_topmed_AN_fin_female=10368;non_topmed_AF_fin_female=0;non_topmed_nhomalt_fin_female=0;non_cancer_AC_fin_female=0;non_cancer_AN_fin_female=10358;non_cancer_AF_fin_female=0;non_cancer_nhomalt_fin_female=0;AC_oth=0;AN_oth=6124;AF_oth=0;nhomalt_oth=0;non_neuro_AC_nfe_male=0;non_neuro_AN_nfe_male=49688;non_neuro_AF_nfe_male=0;non_neuro_nhomalt_nfe_male=0;controls_AC_female=0;controls_AN_female=51260;controls_AF_female=0;controls_nhomalt_female=0;non_cancer_AC_fin=1;non_cancer_AN_fin=21626;non_cancer_AF_fin=4.62406e-05;non_cancer_nhomalt_fin=0;non_topmed_AC_fin=1;non_topmed_AN_fin=21640;non_topmed_AF_fin=4.62107e-05;non_topmed_nhomalt_fin=0;non_cancer_AC_eas_oea=0;non_cancer_AN_eas_oea=13794;non_cancer_AF_eas_oea=0;non_cancer_nhomalt_eas_oea=0;non_topmed_AC_nfe_female=0;non_topmed_AN_nfe_female=48592;non_topmed_AF_nfe_female=0;non_topmed_nhomalt_nfe_female=0;non_cancer_AC_sas_male=0;non_cancer_AN_sas_male=23032;non_cancer_AF_sas_male=0;non_cancer_nhomalt_sas_male=0;controls_AC_asj_male=0;controls_AN_asj_male=1106;controls_AF_asj_male=0;controls_nhomalt_asj_male=0;non_cancer_AC_raw=1;non_cancer_AN_raw=236944;non_cancer_AF_raw=4.22041e-06;non_cancer_nhomalt_raw=0;non_cancer_AC_eas_male=0;non_cancer_AN_eas_male=8744;non_cancer_AF_eas_male=0;non_cancer_nhomalt_eas_male=0;non_topmed_AC_asj_male=0;non_topmed_AN_asj_male=5142;non_topmed_AF_asj_male=0;non_topmed_nhomalt_asj_male=0;non_neuro_AC_oth=0;non_neuro_AN_oth=4858;non_neuro_AF_oth=0;non_neuro_nhomalt_oth=0;AC_male=1;AN_male=135696;AF_male=7.36941e-06;nhomalt_male=0;controls_AC_fin_female=0;controls_AN_fin_female=6474;controls_AF_fin_female=0;controls_nhomalt_fin_female=0;controls_AC_nfe_bgr=0;controls_AN_nfe_bgr=676;controls_AF_nfe_bgr=0;controls_nhomalt_nfe_bgr=0;controls_AC_asj_female=0;controls_AN_asj_female=1214;controls_AF_asj_female=0;controls_nhomalt_asj_female=0;AC_amr_male=0;AN_amr_male=14320;AF_amr_male=0;nhomalt_amr_male=0;AC_amr_female=0;AN_amr_female=20264;AF_amr_female=0;nhomalt_amr_female=0;non_topmed_AC_sas_male=0;non_topmed_AN_sas_male=23072;non_topmed_AF_sas_male=0;non_topmed_nhomalt_sas_male=0;AC_oth_male=0;AN_oth_male=3210;AF_oth_male=0;nhomalt_oth_male=0;non_cancer_AC_sas=0;non_cancer_AN_sas=30526;non_cancer_AF_sas=0;non_cancer_nhomalt_sas=0;non_neuro_AC_nfe_seu=0;non_neuro_AN_nfe_seu=10920;non_neuro_AF_nfe_seu=0;non_neuro_nhomalt_nfe_seu=0;non_cancer_AC_eas_kor=0;non_cancer_AN_eas_kor=3774;non_cancer_AF_eas_kor=0;non_cancer_nhomalt_eas_kor=0;non_topmed_AC_afr_female=0;non_topmed_AN_afr_female=7310;non_topmed_AF_afr_female=0;non_topmed_nhomalt_afr_female=0;controls_AC_sas_male=0;controls_AN_sas_male=11476;controls_AF_sas_male=0;controls_nhomalt_sas_male=0;non_topmed_AC_sas_female=0;non_topmed_AN_sas_female=7544;non_topmed_AF_sas_female=0;non_topmed_nhomalt_sas_female=0;non_topmed_AC_afr=0;non_topmed_AN_afr=11982;non_topmed_AF_afr=0;non_topmed_nhomalt_afr=0;controls_AC=0;controls_AN=109360;controls_AF=0;controls_nhomalt=0;non_neuro_AC_oth_female=0;non_neuro_AN_oth_female=2384;non_neuro_AF_oth_female=0;non_neuro_nhomalt_oth_female=0;non_topmed_faf95_amr=0;non_topmed_faf99_amr=0;faf95_afr=0;faf99_afr=0;faf95_sas=0;faf99_sas=0;controls_faf95_afr=0;controls_faf99_afr=0;faf95_amr=0;faf99_amr=0;non_neuro_faf95_sas=0;non_neuro_faf99_sas=0;faf95_eas=0;faf99_eas=0;faf95=0;faf99=0;non_neuro_faf95_afr=0;non_neuro_faf99_afr=0;non_cancer_faf95_eas=0;non_cancer_faf99_eas=0;non_neuro_faf95_amr=0;non_neuro_faf99_amr=0;non_topmed_faf95_sas=0;non_topmed_faf99_sas=0;controls_faf95_nfe=0;controls_faf99_nfe=0;non_cancer_faf95_afr=0;non_cancer_faf99_afr=0;non_cancer_faf95_amr=0;non_cancer_faf99_amr=0;non_topmed_faf95=0;non_topmed_faf99=0;non_neuro_faf95_nfe=0;non_neuro_faf99_nfe=0;non_neuro_faf95=0;non_neuro_faf99=0;non_topmed_faf95_nfe=0;non_topmed_faf99_nfe=0;controls_faf95_eas=0;controls_faf99_eas=0;controls_faf95_sas=0;controls_faf99_sas=0;faf95_nfe=0;faf99_nfe=0;non_topmed_faf95_eas=0;non_topmed_faf99_eas=0;controls_faf95_amr=0;controls_faf99_amr=0;non_neuro_faf95_eas=0;non_neuro_faf99_eas=0;non_cancer_faf95_nfe=0;non_cancer_faf99_nfe=0;non_cancer_faf95=0;non_cancer_faf99=0;non_cancer_faf95_sas=0;non_cancer_faf99_sas=0;non_topmed_faf95_afr=0;non_topmed_faf99_afr=0;controls_faf95=0;controls_faf99=0;age_hist_het_bin_freq=0|0|0|0|0|0|0|0|0|0;age_hist_het_n_smaller=0;age_hist_het_n_larger=0;age_hist_hom_bin_freq=0|0|0|0|0|0|0|0|0|0;age_hist_hom_n_smaller=0;age_hist_hom_n_larger=0;vep=T|upstream_gene_variant|MODIFIER|CLCNKB|ENSG00000184908|Transcript|ENST00000375667|protein_coding|||||||||||1|287|1||SNV|1|HGNC|2027||||CCDS57974.1|ENSP00000364819|P51801||UPI000046FF10|1|||||||||||||||||||||||||||||||||,T|splice_acceptor_variant|HIGH|CLCNKB|ENSG00000184908|Transcript|ENST00000375679|protein_coding||6/19|ENST00000375679.4:c.577-2A>T||||||||1||1||SNV|1|HGNC|2027|YES|||CCDS168.1|ENSP00000364831|P51801||UPI000040E261|1||||||||||||||||||||||||||||||HC|||INTRON_END:16374998&ACCEPTOR_DISRUPTION_PROB:0.999864730846623&ACCEPTOR_MES_DIFF:8.36675932833517&ACCEPTOR_ESE:17&INTRON_START:16374916&ACCEPTOR_GERP_DIFF:4.68&ACCEPTOR_ISE:16&EXON_START:16374999&BRANCHPOINT_DISTANCE:29&ACCEPTOR_ESS:6&EXON_END:16375077&ACCEPTOR_ISS:7&MUTANT_ACCEPTOR_MES:-4.08773664457014&ACCEPTOR_DISRUPTING&RESCUE_ACCEPTOR_MES:-3.25964205518702&RESCUE_ACCEPTOR_POS:6&CRYPTIC_ACCEPTOR_MES:-2.56278764799603&CRYPTIC_ACCEPTOR_POS:5&INTRON_SIZE:83,T|upstream_gene_variant|MODIFIER|CLCNKB|ENSG00000184908|Transcript|ENST00000431772|protein_coding|||||||||||1|3821|1|cds_start_NF|SNV|1|HGNC|2027|||||ENSP00000389344||Q5T5Q6|UPI000046FF11|1|||||||||||||||||||||||||||||||||
liserjrqlxue commented 3 years ago

I try to use little vcf with rs371756291 to test, but got filter succeed. This is strange. 捕获 top40000.vcf is top 40k lines of gnomAD exome vcf ( which I have normed with hs37d5).

brentp commented 3 years ago

did you use --pass-only? without that, by default, slivar annotates variants that pass your filters, but outputs all variants.

if you can show a single variant where you expression is not working as expected (and preferably the 1 line vcf containing that variant), perhaps I can help.

liserjrqlxue commented 3 years ago

I do not use --pass-only, my cli is like ./slivar expr --js ./highAF.js --info "highAF(INFO)" -v.
Unfortunately, 1 line vcf got what I expected. As I show above and below, It seem that small vcf work well, but large vcf will contain this issue. I'll test farther. 捕获

liserjrqlxue commented 3 years ago

If you have gnomAD exome vcf gnomad.exomes.r2.1.1.sites.vcf.bgz in hand, It's simple to reproduce this issue like below:

zcat gnomad.exomes.r2.1.1.sites.vcf.bgz|head -n40000 > top40000.org.vcf
./slivar expr --js ./highAF.js --info "highAF(INFO)" -v top40000.org.vcf > top40000.org.highAF.vcf
grep rs371756291 top40000.org.highAF.vcf

捕获

top40000.org.highAF.vcf has size of ~1G, I'll try to find smaller exsample. highAF.js as attach file is here with .txt suffix for limitation of github:highAF.js.txt

brentp commented 3 years ago

I will have a look. Thanks for getting a reproducible example.

liserjrqlxue commented 3 years ago

h1000.vcf.gz a little example

liserjrqlxue commented 3 years ago

simple reproducible command: 

./slivar expr --pass-only --info "('AF_popmax' in INFO && INFO.AF_popmax>=0.9)||INFO.AF>=0.9" -v h1000.vcf.gz|grep -w rs371756291

捕获

liserjrqlxue commented 3 years ago

It seems that rs371756291 meet rules of "'AF_popmax' in INFO && INFO.AF_popmax>=0.9", even though it does not have AF_popmax field. 捕获

brentp commented 3 years ago

Thanks for narrowing this down. I have found the problem and committed a fix. It will be out in next release. Meanwhile, here is an updated binary if you want to try it out. Thanks again!

slivar.gz

liserjrqlxue commented 3 years ago

This issue seems fixed. After redo, 529 extra variants filtered, and only keep 2 varint without AF_popmax field. 捕获 捕获

brentp commented 3 years ago

This is out in latest release: https://github.com/brentp/slivar/releases/tag/v0.1.13

thanks again for tracking this down and for the clear test-case.