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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
61501-61550 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.4277 | 99.0173 | 99.8415 | 46.1817 | 2519 | 25 | 2519 | 4 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.8700 | 99.7836 | 99.9566 | 69.9578 | 11527 | 25 | 11527 | 5 | 3 | 60.0000 | |
| hfeng-pmm3 | INDEL | * | map_l125_m1_e0 | het | 98.2769 | 98.1273 | 98.4270 | 85.5800 | 1310 | 25 | 1314 | 21 | 3 | 14.2857 | |
| hfeng-pmm3 | INDEL | * | segdup | * | 99.3329 | 99.0219 | 99.6459 | 93.8860 | 2531 | 25 | 2533 | 9 | 3 | 33.3333 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 98.3798 | 96.8112 | 100.0000 | 33.4921 | 759 | 25 | 838 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.6557 | 99.3868 | 99.9261 | 40.5247 | 4052 | 25 | 4055 | 3 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.0206 | 99.3362 | 98.7071 | 54.3318 | 3741 | 25 | 3741 | 49 | 45 | 91.8367 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.0206 | 99.3362 | 98.7071 | 54.3318 | 3741 | 25 | 3741 | 49 | 45 | 91.8367 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.9161 | 92.6686 | 99.3994 | 59.6852 | 316 | 25 | 331 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | * | homalt | 98.2839 | 99.5993 | 97.0028 | 48.9358 | 6214 | 25 | 6214 | 192 | 191 | 99.4792 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 89.7527 | 83.5526 | 96.9466 | 91.3302 | 127 | 25 | 127 | 4 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 99.2980 | 99.5114 | 99.0854 | 41.3691 | 5092 | 25 | 5092 | 47 | 47 | 100.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 98.0392 | 96.1538 | 100.0000 | 23.3374 | 625 | 25 | 634 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | D1_5 | map_l150_m2_e1 | * | 97.9841 | 96.7866 | 99.2116 | 86.8612 | 753 | 25 | 755 | 6 | 1 | 16.6667 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.9161 | 92.6686 | 99.3994 | 59.8795 | 316 | 25 | 331 | 2 | 2 | 100.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.8663 | 91.3194 | 94.4664 | 79.0041 | 263 | 25 | 239 | 14 | 8 | 57.1429 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.2669 | 96.0317 | 98.5342 | 65.6983 | 605 | 25 | 605 | 9 | 6 | 66.6667 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.9955 | 99.0692 | 98.9219 | 52.5490 | 2661 | 25 | 2661 | 29 | 0 | 0.0000 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.3331 | 99.7813 | 95.0021 | 46.2479 | 11408 | 25 | 11405 | 600 | 4 | 0.6667 | |
| jlack-gatk | SNP | * | map_l250_m0_e0 | homalt | 97.4194 | 96.0254 | 98.8543 | 92.0297 | 604 | 25 | 604 | 7 | 4 | 57.1429 | |
| jlack-gatk | SNP | tv | HG002compoundhet | het | 98.9462 | 99.4650 | 98.4329 | 56.5753 | 4648 | 25 | 4648 | 74 | 14 | 18.9189 | |
| jli-custom | INDEL | * | map_l150_m1_e0 | * | 98.3164 | 98.1315 | 98.5019 | 88.5230 | 1313 | 25 | 1315 | 20 | 7 | 35.0000 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 94.7739 | 90.6810 | 99.2537 | 66.3317 | 253 | 26 | 266 | 2 | 1 | 50.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.7368 | 90.3346 | 99.5902 | 76.0314 | 243 | 26 | 243 | 1 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I1_5 | map_siren | het | 96.7640 | 98.4533 | 95.1317 | 84.9119 | 1655 | 26 | 1661 | 85 | 5 | 5.8824 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.4586 | 99.0170 | 97.9065 | 84.2545 | 2619 | 26 | 2619 | 56 | 14 | 25.0000 | |
| jlack-gatk | SNP | tv | map_l250_m0_e0 | * | 89.3051 | 96.6013 | 83.0337 | 95.8027 | 739 | 26 | 739 | 151 | 9 | 5.9603 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.4480 | 99.1333 | 99.7647 | 74.0763 | 2974 | 26 | 2968 | 7 | 3 | 42.8571 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 98.5175 | 97.1831 | 99.8891 | 27.3167 | 897 | 26 | 901 | 1 | 1 | 100.0000 | |
| jli-custom | INDEL | * | map_l125_m1_e0 | het | 98.3481 | 98.0524 | 98.6456 | 86.0194 | 1309 | 26 | 1311 | 18 | 4 | 22.2222 | |
| jli-custom | INDEL | * | map_l150_m2_e0 | * | 98.3640 | 98.1534 | 98.5755 | 89.3077 | 1382 | 26 | 1384 | 20 | 7 | 35.0000 | |
| hfeng-pmm3 | INDEL | * | map_l100_m0_e0 | * | 98.2754 | 98.3365 | 98.2143 | 84.4120 | 1537 | 26 | 1540 | 28 | 6 | 21.4286 | |
| hfeng-pmm1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 90.0000 | 82.8947 | 98.4375 | 90.7581 | 126 | 26 | 126 | 2 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | * | segdup | * | 99.0994 | 98.9828 | 99.2163 | 94.4475 | 2530 | 26 | 2532 | 20 | 4 | 20.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 77.9859 | 92.7577 | 67.2727 | 45.6641 | 333 | 26 | 333 | 162 | 160 | 98.7654 | |
| jlack-gatk | INDEL | * | map_l125_m2_e0 | het | 92.6228 | 98.1308 | 87.7002 | 91.9195 | 1365 | 26 | 1369 | 192 | 9 | 4.6875 | |
| jlack-gatk | INDEL | * | map_l125_m2_e1 | het | 92.6447 | 98.1534 | 87.7215 | 91.9821 | 1382 | 26 | 1386 | 194 | 9 | 4.6392 | |
| jlack-gatk | INDEL | * | map_l150_m1_e0 | * | 93.5297 | 98.0568 | 89.4022 | 92.0707 | 1312 | 26 | 1316 | 156 | 9 | 5.7692 | |
| jlack-gatk | INDEL | * | map_l150_m2_e0 | * | 93.7096 | 98.1534 | 89.6507 | 92.6142 | 1382 | 26 | 1386 | 160 | 9 | 5.6250 | |
| jlack-gatk | INDEL | * | map_siren | homalt | 99.0590 | 99.0207 | 99.0974 | 80.4586 | 2629 | 26 | 2635 | 24 | 14 | 58.3333 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.2345 | 95.7792 | 96.6942 | 67.4731 | 590 | 26 | 585 | 20 | 16 | 80.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 98.3139 | 96.6837 | 100.0000 | 33.5714 | 758 | 26 | 837 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.3623 | 98.8621 | 99.8675 | 43.6567 | 2259 | 26 | 2262 | 3 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 75.8784 | 82.4324 | 70.2899 | 72.7811 | 122 | 26 | 97 | 41 | 41 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.5799 | 90.9722 | 96.3415 | 79.3277 | 262 | 26 | 237 | 9 | 5 | 55.5556 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.8615 | 98.0480 | 99.6885 | 70.4692 | 1306 | 26 | 1280 | 4 | 2 | 50.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.2559 | 99.3087 | 99.2032 | 69.9329 | 3735 | 26 | 3735 | 30 | 29 | 96.6667 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.2118 | 90.9722 | 95.5645 | 79.3505 | 262 | 26 | 237 | 11 | 7 | 63.6364 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.2559 | 99.3087 | 99.2032 | 69.9329 | 3735 | 26 | 3735 | 30 | 29 | 96.6667 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.8372 | 97.7011 | 100.0000 | 42.2937 | 1105 | 26 | 1112 | 0 | 0 | ||