PrecisionFDA
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Explore HG002 comparison results
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| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
14951-15000 / 86044 show all | |||||||||||||||
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 66.8725 | 51.0638 | 96.8586 | 35.5002 | 288 | 276 | 1480 | 48 | 47 | 97.9167 | |
| gduggal-snapvard | INDEL | I1_5 | map_l250_m2_e0 | * | 84.1683 | 92.9204 | 76.9231 | 95.9931 | 105 | 8 | 160 | 48 | 13 | 27.0833 | |
| gduggal-snapvard | INDEL | I1_5 | map_l250_m2_e1 | * | 84.2599 | 92.9825 | 77.0335 | 96.0759 | 106 | 8 | 161 | 48 | 13 | 27.0833 | |
| gduggal-snapvard | INDEL | I6_15 | map_l100_m0_e0 | * | 57.3585 | 57.5758 | 57.1429 | 81.9063 | 19 | 14 | 64 | 48 | 36 | 75.0000 | |
| gduggal-snapvard | INDEL | I6_15 | map_l100_m0_e0 | het | 68.5015 | 94.1176 | 53.8462 | 81.9757 | 16 | 1 | 56 | 48 | 36 | 75.0000 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 94.7012 | 90.7431 | 99.0204 | 73.2912 | 4921 | 502 | 4852 | 48 | 28 | 58.3333 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 83.8207 | 76.4233 | 92.8036 | 43.9496 | 1141 | 352 | 619 | 48 | 37 | 77.0833 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 66.4101 | 59.5041 | 75.1295 | 58.0435 | 144 | 98 | 145 | 48 | 41 | 85.4167 | |
| gduggal-snapplat | INDEL | D1_5 | map_l125_m0_e0 | * | 83.1468 | 77.2177 | 90.0621 | 94.3416 | 383 | 113 | 435 | 48 | 13 | 27.0833 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 42.0587 | 30.6709 | 66.8966 | 62.3377 | 96 | 217 | 97 | 48 | 42 | 87.5000 | |
| gduggal-bwavard | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 85.7527 | 75.1764 | 99.7922 | 61.3457 | 23125 | 7636 | 23046 | 48 | 38 | 79.1667 | |
| gduggal-bwavard | INDEL | D16_PLUS | map_l100_m1_e0 | * | 54.0541 | 57.4713 | 51.0204 | 92.8363 | 50 | 37 | 50 | 48 | 21 | 43.7500 | |
| gduggal-bwavard | INDEL | D16_PLUS | map_l100_m2_e0 | het | 61.8474 | 87.5000 | 47.8261 | 93.3765 | 42 | 6 | 44 | 48 | 20 | 41.6667 | |
| gduggal-bwavard | INDEL | D6_15 | segdup | * | 68.8950 | 65.9686 | 72.0930 | 94.5707 | 126 | 65 | 124 | 48 | 48 | 100.0000 | |
| gduggal-bwavard | INDEL | D6_15 | segdup | het | 77.0066 | 95.6522 | 64.4444 | 95.1837 | 88 | 4 | 87 | 48 | 48 | 100.0000 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 52.1569 | 63.6364 | 44.1860 | 82.8000 | 42 | 24 | 38 | 48 | 24 | 50.0000 | |
| eyeh-varpipe | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7381 | 99.9188 | 99.5581 | 52.7387 | 11075 | 9 | 10815 | 48 | 16 | 33.3333 | |
| eyeh-varpipe | SNP | tv | * | hetalt | 99.3621 | 99.8852 | 98.8445 | 45.4641 | 870 | 1 | 4106 | 48 | 46 | 95.8333 | |
| eyeh-varpipe | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 92.0089 | 95.6607 | 88.6256 | 77.9404 | 485 | 22 | 374 | 48 | 17 | 35.4167 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 83.2899 | 84.1808 | 82.4176 | 55.5375 | 149 | 28 | 225 | 48 | 45 | 93.7500 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 87.7499 | 80.8367 | 95.9562 | 58.8989 | 599 | 142 | 1139 | 48 | 25 | 52.0833 | |
| gduggal-bwavard | SNP | * | map_siren | homalt | 98.4056 | 96.9468 | 99.9088 | 52.1457 | 53472 | 1684 | 52608 | 48 | 40 | 83.3333 | |
| asubramanian-gatk | INDEL | D1_5 | HG002complexvar | hetalt | 94.5568 | 92.7515 | 96.4339 | 73.6698 | 1254 | 98 | 1298 | 48 | 47 | 97.9167 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.7489 | 95.0355 | 96.4732 | 75.4199 | 1340 | 70 | 1313 | 48 | 37 | 77.0833 | |
| asubramanian-gatk | INDEL | D1_5 | map_l125_m1_e0 | het | 89.7485 | 86.7769 | 92.9308 | 90.5838 | 630 | 96 | 631 | 48 | 4 | 8.3333 | |
| asubramanian-gatk | INDEL | D1_5 | map_l125_m2_e0 | het | 89.8280 | 86.6492 | 93.2489 | 90.9553 | 662 | 102 | 663 | 48 | 4 | 8.3333 | |
| asubramanian-gatk | INDEL | D1_5 | map_l125_m2_e1 | het | 89.9101 | 86.7532 | 93.3054 | 91.0049 | 668 | 102 | 669 | 48 | 4 | 8.3333 | |
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9634 | 98.0991 | 99.8431 | 67.2451 | 30551 | 592 | 30551 | 48 | 17 | 35.4167 | |
| astatham-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9634 | 98.0991 | 99.8431 | 67.2451 | 30551 | 592 | 30551 | 48 | 17 | 35.4167 | |
| astatham-gatk | SNP | ti | map_l150_m2_e0 | * | 91.3750 | 84.3165 | 99.7232 | 79.9461 | 17295 | 3217 | 17291 | 48 | 27 | 56.2500 | |
| astatham-gatk | SNP | ti | map_l150_m2_e1 | * | 91.3679 | 84.3025 | 99.7259 | 80.0126 | 17470 | 3253 | 17466 | 48 | 27 | 56.2500 | |
| astatham-gatk | SNP | tv | map_l100_m2_e1 | * | 91.8357 | 85.0651 | 99.7773 | 71.9862 | 21507 | 3776 | 21503 | 48 | 16 | 33.3333 | |
| asubramanian-gatk | INDEL | C1_5 | HG002compoundhet | homalt | 0.0000 | 0.0000 | 34.2466 | 0 | 0 | 0 | 48 | 0 | 0.0000 | ||
| anovak-vg | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 47.6231 | 55.9322 | 41.4634 | 53.9326 | 33 | 26 | 34 | 48 | 35 | 72.9167 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.7394 | 96.9504 | 96.5293 | 75.1304 | 1367 | 43 | 1335 | 48 | 39 | 81.2500 | |
| asubramanian-gatk | SNP | tv | segdup | het | 97.9042 | 96.7657 | 99.0698 | 94.3222 | 5116 | 171 | 5112 | 48 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.5826 | 97.4026 | 97.7633 | 76.4020 | 2100 | 56 | 2098 | 48 | 23 | 47.9167 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.1646 | 92.9308 | 99.6316 | 30.7725 | 12791 | 973 | 12982 | 48 | 48 | 100.0000 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 17.8914 | 14.8148 | 22.5806 | 56.6434 | 16 | 92 | 14 | 48 | 8 | 16.6667 | |
| hfeng-pmm1 | SNP | tv | map_l100_m2_e1 | het | 99.4686 | 99.2408 | 99.6974 | 66.3712 | 15817 | 121 | 15813 | 48 | 12 | 25.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | HG002compoundhet | homalt | 11.1111 | 100.0000 | 5.8824 | 76.6055 | 3 | 0 | 3 | 48 | 47 | 97.9167 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.0521 | 96.8708 | 99.2627 | 50.9309 | 6470 | 209 | 6462 | 48 | 45 | 93.7500 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 91.0253 | 90.5074 | 91.5493 | 68.7397 | 553 | 58 | 520 | 48 | 46 | 95.8333 | |
| jlack-gatk | INDEL | I1_5 | map_l125_m2_e1 | het | 94.5144 | 98.0315 | 91.2409 | 91.8416 | 498 | 10 | 500 | 48 | 3 | 6.2500 | |
| hfeng-pmm2 | SNP | * | map_l250_m0_e0 | het | 97.4257 | 98.0080 | 96.8504 | 93.8031 | 1476 | 30 | 1476 | 48 | 4 | 8.3333 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 91.1080 | 90.6710 | 91.5493 | 68.5493 | 554 | 57 | 520 | 48 | 46 | 95.8333 | |
| hfeng-pmm3 | INDEL | I16_PLUS | * | homalt | 98.1968 | 99.4234 | 97.0000 | 68.6397 | 1552 | 9 | 1552 | 48 | 45 | 93.7500 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.8671 | 92.3787 | 99.6294 | 28.3565 | 12715 | 1049 | 12903 | 48 | 48 | 100.0000 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.8065 | 92.2605 | 99.6360 | 30.7769 | 12946 | 1086 | 13139 | 48 | 48 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D1_5 | HG002compoundhet | het | 96.9264 | 96.5856 | 97.2696 | 68.4720 | 1669 | 59 | 1710 | 48 | 21 | 43.7500 | |