PrecisionFDA
Truth Challenge
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
71051-71100 / 86044 show all | |||||||||||||||
| 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 | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 47.6231 | 55.9322 | 41.4634 | 53.9326 | 33 | 26 | 34 | 48 | 35 | 72.9167 | |
| 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 | |
| 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 | |
| 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-bwavard | SNP | * | map_siren | homalt | 98.4056 | 96.9468 | 99.9088 | 52.1457 | 53472 | 1684 | 52608 | 48 | 40 | 83.3333 | |
| gduggal-bwavard | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 85.7527 | 75.1764 | 99.7922 | 61.3457 | 23125 | 7636 | 23046 | 48 | 38 | 79.1667 | |
| dgrover-gatk | INDEL | * | map_l100_m2_e0 | het | 98.1424 | 98.3528 | 97.9328 | 87.3523 | 2269 | 38 | 2274 | 48 | 10 | 20.8333 | |
| dgrover-gatk | INDEL | * | map_l100_m2_e1 | het | 98.1708 | 98.3781 | 97.9644 | 87.4166 | 2305 | 38 | 2310 | 48 | 10 | 20.8333 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 96.8519 | 94.5071 | 99.3160 | 27.2218 | 6951 | 404 | 6970 | 48 | 31 | 64.5833 | |
| ckim-isaac | SNP | * | map_l150_m2_e1 | het | 74.2817 | 59.2251 | 99.6036 | 80.2344 | 12060 | 8303 | 12061 | 48 | 9 | 18.7500 | |
| ckim-vqsr | INDEL | * | map_l150_m1_e0 | * | 96.2213 | 96.0389 | 96.4045 | 93.0291 | 1285 | 53 | 1287 | 48 | 6 | 12.5000 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 96.8939 | 95.6734 | 98.1460 | 66.3548 | 2543 | 115 | 2541 | 48 | 16 | 33.3333 | |
| dgrover-gatk | SNP | tv | map_l250_m1_e0 | * | 98.0711 | 97.9600 | 98.1825 | 89.6431 | 2593 | 54 | 2593 | 48 | 11 | 22.9167 | |
| egarrison-hhga | INDEL | * | segdup | * | 97.9435 | 97.7700 | 98.1176 | 98.6833 | 2499 | 57 | 2502 | 48 | 36 | 75.0000 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 88.5339 | 85.2853 | 92.0398 | 83.8251 | 568 | 98 | 555 | 48 | 27 | 56.2500 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 88.5339 | 85.2853 | 92.0398 | 83.8251 | 568 | 98 | 555 | 48 | 27 | 56.2500 | |
| egarrison-hhga | INDEL | I1_5 | HG002compoundhet | hetalt | 97.3530 | 95.2492 | 99.5519 | 56.2316 | 10646 | 531 | 10663 | 48 | 44 | 91.6667 | |
| egarrison-hhga | SNP | * | map_l125_m0_e0 | * | 99.2012 | 98.6588 | 99.7496 | 73.5088 | 19125 | 260 | 19125 | 48 | 23 | 47.9167 | |
| egarrison-hhga | SNP | ti | map_l125_m1_e0 | * | 99.4628 | 99.0932 | 99.8351 | 68.9921 | 29069 | 266 | 29069 | 48 | 24 | 50.0000 | |
| egarrison-hhga | SNP | tv | map_l100_m2_e0 | * | 99.4951 | 99.1851 | 99.8071 | 65.1309 | 24829 | 204 | 24829 | 48 | 19 | 39.5833 | |
| egarrison-hhga | SNP | tv | map_l100_m2_e1 | * | 99.4981 | 99.1892 | 99.8090 | 65.1604 | 25078 | 205 | 25078 | 48 | 19 | 39.5833 | |
| 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-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 | |
| 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 | |
| hfeng-pmm2 | SNP | * | map_l250_m0_e0 | het | 97.4257 | 98.0080 | 96.8504 | 93.8031 | 1476 | 30 | 1476 | 48 | 4 | 8.3333 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.7759 | 97.0213 | 96.5318 | 75.2636 | 1368 | 42 | 1336 | 48 | 39 | 81.2500 | |
| ciseli-custom | INDEL | I1_5 | map_l150_m0_e0 | het | 59.3607 | 61.3208 | 57.5221 | 94.3500 | 65 | 41 | 65 | 48 | 38 | 79.1667 | |
| ckim-dragen | INDEL | I1_5 | segdup | het | 95.3418 | 99.2565 | 91.7241 | 96.0707 | 534 | 4 | 532 | 48 | 1 | 2.0833 | |
| ckim-dragen | SNP | ti | map_l250_m0_e0 | het | 95.1974 | 95.5032 | 94.8936 | 94.2165 | 892 | 42 | 892 | 48 | 1 | 2.0833 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0364 | 98.8318 | 99.2419 | 76.8770 | 6345 | 75 | 6284 | 48 | 25 | 52.0833 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.8875 | 94.6157 | 99.2711 | 52.0847 | 6537 | 372 | 6537 | 48 | 43 | 89.5833 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0364 | 98.8318 | 99.2419 | 76.8770 | 6345 | 75 | 6284 | 48 | 25 | 52.0833 | |
| ckim-gatk | INDEL | I6_15 | HG002compoundhet | het | 86.2400 | 97.5962 | 77.2512 | 84.6657 | 203 | 5 | 163 | 48 | 47 | 97.9167 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.5044 | 99.4538 | 99.5551 | 80.0137 | 10742 | 59 | 10742 | 48 | 17 | 35.4167 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 80.7906 | 68.5669 | 98.3181 | 40.6653 | 2622 | 1202 | 2806 | 48 | 41 | 85.4167 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.2224 | 98.6702 | 93.8931 | 48.2213 | 742 | 10 | 738 | 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 | |