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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
18401-18450 / 86044 show all | |||||||||||||||
| gduggal-bwafb | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.6797 | 99.7436 | 99.6160 | 62.2679 | 7001 | 18 | 7004 | 27 | 15 | 55.5556 | |
| gduggal-bwaplat | INDEL | * | map_l100_m1_e0 | * | 80.3840 | 67.7078 | 98.9002 | 92.0959 | 2428 | 1158 | 2428 | 27 | 10 | 37.0370 | |
| gduggal-bwavard | INDEL | C1_5 | map_l150_m2_e0 | * | 0.0000 | 0.0000 | 41.3043 | 96.3434 | 0 | 0 | 19 | 27 | 3 | 11.1111 | |
| gduggal-bwavard | INDEL | C1_5 | map_l150_m2_e0 | het | 0.0000 | 0.0000 | 32.5000 | 96.4093 | 0 | 0 | 13 | 27 | 3 | 11.1111 | |
| gduggal-bwavard | INDEL | C1_5 | map_l150_m2_e1 | * | 0.0000 | 0.0000 | 42.5532 | 96.3509 | 0 | 0 | 20 | 27 | 3 | 11.1111 | |
| gduggal-bwavard | INDEL | C1_5 | map_l150_m2_e1 | het | 0.0000 | 0.0000 | 34.1463 | 96.4004 | 0 | 0 | 14 | 27 | 3 | 11.1111 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | het | 20.5128 | 50.0000 | 12.9032 | 57.5342 | 4 | 4 | 4 | 27 | 26 | 96.2963 | |
| gduggal-bwavard | INDEL | D6_15 | map_l100_m0_e0 | * | 73.5260 | 73.7864 | 73.2673 | 91.6529 | 76 | 27 | 74 | 27 | 20 | 74.0741 | |
| gduggal-bwavard | INDEL | D6_15 | map_l100_m0_e0 | het | 81.3793 | 100.0000 | 68.6047 | 92.0591 | 60 | 0 | 59 | 27 | 20 | 74.0741 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 24.8564 | 19.5402 | 34.1463 | 81.7778 | 17 | 70 | 14 | 27 | 16 | 59.2593 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 44.2791 | 62.9630 | 34.1463 | 81.0185 | 17 | 10 | 14 | 27 | 16 | 59.2593 | |
| gduggal-bwavard | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.1182 | 98.6758 | 99.5645 | 45.6045 | 6185 | 83 | 6173 | 27 | 13 | 48.1481 | |
| gduggal-snapfb | INDEL | * | segdup | homalt | 95.2260 | 93.4375 | 97.0842 | 94.2949 | 897 | 63 | 899 | 27 | 15 | 55.5556 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 82.7273 | 89.2157 | 77.1186 | 54.2636 | 91 | 11 | 91 | 27 | 27 | 100.0000 | |
| gduggal-bwafb | INDEL | D1_5 | HG002compoundhet | hetalt | 93.3119 | 88.0482 | 99.2450 | 76.1026 | 8995 | 1221 | 3549 | 27 | 27 | 100.0000 | |
| dgrover-gatk | INDEL | * | segdup | * | 99.0625 | 99.1784 | 98.9470 | 94.7737 | 2535 | 21 | 2537 | 27 | 10 | 37.0370 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.6877 | 99.7767 | 99.5988 | 53.6597 | 6701 | 15 | 6703 | 27 | 8 | 29.6296 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.4203 | 98.9214 | 95.9641 | 68.3987 | 642 | 7 | 642 | 27 | 27 | 100.0000 | |
| dgrover-gatk | SNP | ti | HG002compoundhet | * | 99.8369 | 99.8284 | 99.8455 | 35.6925 | 17448 | 30 | 17446 | 27 | 21 | 77.7778 | |
| ckim-isaac | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.1734 | 94.6284 | 99.8591 | 48.1340 | 19114 | 1085 | 19138 | 27 | 18 | 66.6667 | |
| ckim-isaac | SNP | * | map_l125_m0_e0 | * | 70.7547 | 54.8207 | 99.7466 | 75.5092 | 10627 | 8758 | 10627 | 27 | 5 | 18.5185 | |
| ckim-isaac | SNP | ti | map_l150_m2_e1 | het | 75.7313 | 61.0680 | 99.6614 | 80.0450 | 7948 | 5067 | 7948 | 27 | 3 | 11.1111 | |
| ckim-isaac | SNP | tv | map_l125_m1_e0 | het | 74.2974 | 59.2633 | 99.5522 | 74.3164 | 6001 | 4125 | 6003 | 27 | 7 | 25.9259 | |
| ckim-vqsr | INDEL | * | map_l250_m1_e0 | * | 93.0757 | 94.7541 | 91.4557 | 97.2688 | 289 | 16 | 289 | 27 | 2 | 7.4074 | |
| ckim-vqsr | INDEL | * | map_l250_m2_e0 | * | 93.4524 | 94.8640 | 92.0821 | 97.4260 | 314 | 17 | 314 | 27 | 2 | 7.4074 | |
| ckim-vqsr | INDEL | * | map_l250_m2_e1 | * | 93.4911 | 94.8949 | 92.1283 | 97.4798 | 316 | 17 | 316 | 27 | 2 | 7.4074 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.4580 | 95.5784 | 99.4130 | 24.4663 | 4561 | 211 | 4573 | 27 | 27 | 100.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.5454 | 94.9673 | 98.1769 | 85.0222 | 1453 | 77 | 1454 | 27 | 18 | 66.6667 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.5454 | 94.9673 | 98.1769 | 85.0222 | 1453 | 77 | 1454 | 27 | 18 | 66.6667 | |
| ckim-vqsr | SNP | ti | func_cds | * | 99.7642 | 99.7244 | 99.8040 | 29.1716 | 13749 | 38 | 13747 | 27 | 0 | 0.0000 | |
| ckim-vqsr | SNP | ti | func_cds | het | 99.7473 | 99.8119 | 99.6828 | 33.7510 | 8488 | 16 | 8486 | 27 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l100_m1_e0 | het | 98.0207 | 98.2630 | 97.7796 | 82.5011 | 1188 | 21 | 1189 | 27 | 7 | 25.9259 | |
| egarrison-hhga | INDEL | D1_5 | map_l100_m2_e0 | het | 98.0946 | 98.3280 | 97.8622 | 83.1891 | 1235 | 21 | 1236 | 27 | 7 | 25.9259 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 85.8238 | 91.8033 | 80.5755 | 80.1994 | 112 | 10 | 112 | 27 | 16 | 59.2593 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 85.5570 | 79.7101 | 92.3295 | 70.6177 | 330 | 84 | 325 | 27 | 17 | 62.9630 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.6158 | 95.9792 | 99.3093 | 24.9856 | 3867 | 162 | 3882 | 27 | 26 | 96.2963 | |
| egarrison-hhga | SNP | * | map_l250_m1_e0 | het | 98.2228 | 97.0557 | 99.4184 | 88.3044 | 4615 | 140 | 4615 | 27 | 10 | 37.0370 | |
| egarrison-hhga | SNP | * | map_siren | homalt | 99.8639 | 99.7770 | 99.9510 | 53.4112 | 55033 | 123 | 55033 | 27 | 24 | 88.8889 | |
| egarrison-hhga | SNP | tv | map_l150_m2_e0 | * | 99.2922 | 98.8287 | 99.7600 | 74.2574 | 11222 | 133 | 11222 | 27 | 12 | 44.4444 | |
| egarrison-hhga | SNP | tv | map_l150_m2_e1 | * | 99.3012 | 98.8437 | 99.7631 | 74.2719 | 11369 | 133 | 11369 | 27 | 12 | 44.4444 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 88.1005 | 80.0000 | 98.0263 | 81.2243 | 428 | 107 | 1341 | 27 | 27 | 100.0000 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 72.1649 | 94.3008 | 0 | 0 | 70 | 27 | 25 | 92.5926 | |
| gduggal-snapvard | INDEL | C16_PLUS | HG002complexvar | het | 0.0000 | 0.0000 | 37.2093 | 71.1409 | 0 | 0 | 16 | 27 | 5 | 18.5185 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.7435 | 93.5247 | 98.0701 | 82.9494 | 1401 | 97 | 1372 | 27 | 13 | 48.1481 | |
| gduggal-snapplat | INDEL | I1_5 | map_l125_m0_e0 | het | 80.9783 | 77.6042 | 84.6591 | 95.8412 | 149 | 43 | 149 | 27 | 0 | 0.0000 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 88.3912 | 83.6820 | 93.6620 | 67.7273 | 400 | 78 | 399 | 27 | 22 | 81.4815 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.0203 | 98.2985 | 99.7527 | 60.4577 | 10919 | 189 | 10893 | 27 | 9 | 33.3333 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 95.4941 | 94.2149 | 96.8085 | 80.8641 | 912 | 56 | 819 | 27 | 18 | 66.6667 | |
| hfeng-pmm1 | INDEL | * | map_l100_m0_e0 | * | 97.6521 | 97.0569 | 98.2547 | 83.9206 | 1517 | 46 | 1520 | 27 | 6 | 22.2222 | |
| hfeng-pmm1 | INDEL | * | map_l100_m1_e0 | het | 97.8105 | 96.8680 | 98.7716 | 82.6711 | 2165 | 70 | 2171 | 27 | 4 | 14.8148 | |