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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
34501-34550 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | SNP | ti | map_l125_m1_e0 | * | 99.1074 | 98.4080 | 99.8167 | 62.4199 | 28868 | 467 | 28869 | 53 | 19 | 35.8491 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 100.0000 | 100.0000 | 100.0000 | 62.4204 | 59 | 0 | 59 | 0 | 0 | ||
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 44.0199 | 83.7017 | 29.8625 | 62.4216 | 303 | 59 | 304 | 714 | 698 | 97.7591 | |
| jlack-gatk | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8006 | 99.8575 | 99.7437 | 62.4217 | 7009 | 10 | 7005 | 18 | 3 | 16.6667 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 88.0745 | 87.7173 | 88.4346 | 62.4232 | 757 | 106 | 757 | 99 | 93 | 93.9394 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.4130 | 97.1455 | 97.6820 | 62.4233 | 42098 | 1237 | 41887 | 994 | 949 | 95.4728 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.9199 | 95.6831 | 98.1890 | 62.4288 | 13986 | 631 | 13609 | 251 | 218 | 86.8526 | |
| dgrover-gatk | INDEL | I1_5 | * | hetalt | 97.2805 | 94.7387 | 99.9625 | 62.4322 | 10606 | 589 | 10669 | 4 | 4 | 100.0000 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 25.7297 | 17.3354 | 49.8866 | 62.4361 | 229 | 1092 | 220 | 221 | 16 | 7.2398 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.0389 | 96.6511 | 99.4672 | 62.4367 | 6205 | 215 | 11948 | 64 | 47 | 73.4375 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.0389 | 96.6511 | 99.4672 | 62.4367 | 6205 | 215 | 11948 | 64 | 47 | 73.4375 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 75.6587 | 80.6700 | 71.2335 | 62.4381 | 3034 | 727 | 2974 | 1201 | 1094 | 91.0908 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 75.6587 | 80.6700 | 71.2335 | 62.4381 | 3034 | 727 | 2974 | 1201 | 1094 | 91.0908 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.9904 | 94.8590 | 99.2198 | 62.4389 | 2288 | 124 | 2289 | 18 | 13 | 72.2222 | |
| gduggal-snapvard | SNP | ti | map_l100_m2_e1 | homalt | 97.9449 | 96.1825 | 99.7730 | 62.4406 | 17788 | 706 | 17584 | 40 | 33 | 82.5000 | |
| rpoplin-dv42 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 90.8516 | 83.6115 | 99.4643 | 62.4413 | 551 | 108 | 557 | 3 | 3 | 100.0000 | |
| rpoplin-dv42 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 90.8516 | 83.6115 | 99.4643 | 62.4413 | 551 | 108 | 557 | 3 | 3 | 100.0000 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 64.6126 | 88.1402 | 50.9992 | 62.4437 | 654 | 88 | 638 | 613 | 589 | 96.0848 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.8372 | 98.8372 | 98.8372 | 62.4454 | 255 | 3 | 255 | 3 | 2 | 66.6667 | |
| cchapple-custom | SNP | tv | map_l125_m1_e0 | homalt | 98.4050 | 96.8601 | 100.0000 | 62.4454 | 5676 | 184 | 5673 | 0 | 0 | ||
| gduggal-snapvard | SNP | ti | map_l100_m2_e0 | homalt | 97.9436 | 96.1822 | 99.7707 | 62.4459 | 17610 | 699 | 17408 | 40 | 33 | 82.5000 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 68.8773 | 63.7081 | 74.9595 | 62.4506 | 5326 | 3034 | 5550 | 1854 | 1409 | 75.9978 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 68.8773 | 63.7081 | 74.9595 | 62.4506 | 5326 | 3034 | 5550 | 1854 | 1409 | 75.9978 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.5026 | 97.4692 | 99.5582 | 62.4506 | 1502 | 39 | 4732 | 21 | 16 | 76.1905 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 81.3153 | 78.8474 | 83.9428 | 62.4516 | 2531 | 679 | 2525 | 483 | 481 | 99.5859 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 94.1085 | 98.8889 | 89.7690 | 62.4535 | 267 | 3 | 272 | 31 | 1 | 3.2258 | |
| jpowers-varprowl | SNP | tv | HG002compoundhet | het | 92.4509 | 89.4714 | 95.6356 | 62.4569 | 4181 | 492 | 4273 | 195 | 18 | 9.2308 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.0897 | 98.4762 | 99.7110 | 62.4593 | 1034 | 16 | 1035 | 3 | 3 | 100.0000 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 65.7441 | 83.6158 | 54.1667 | 62.4609 | 148 | 29 | 195 | 165 | 113 | 68.4848 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.2513 | 95.6140 | 94.8913 | 62.4643 | 872 | 40 | 873 | 47 | 32 | 68.0851 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 94.3185 | 92.1152 | 96.6299 | 62.4649 | 4895 | 419 | 4903 | 171 | 122 | 71.3450 | |
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5619 | 99.3100 | 99.8151 | 62.4675 | 2159 | 15 | 2159 | 4 | 0 | 0.0000 | |
| jli-custom | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 99.7133 | 99.4851 | 99.9425 | 62.4676 | 1739 | 9 | 1739 | 1 | 1 | 100.0000 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.5873 | 97.9738 | 99.2084 | 62.4678 | 3820 | 79 | 3760 | 30 | 27 | 90.0000 | |
| ltrigg-rtg1 | SNP | * | map_l100_m2_e1 | homalt | 99.8200 | 99.7446 | 99.8955 | 62.4711 | 27725 | 71 | 27724 | 29 | 26 | 89.6552 | |
| hfeng-pmm1 | SNP | tv | map_l100_m1_e0 | homalt | 99.8507 | 99.8452 | 99.8562 | 62.4720 | 9029 | 14 | 9029 | 13 | 5 | 38.4615 | |
| jpowers-varprowl | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 49.6437 | 72.3762 | 37.7781 | 62.4735 | 2924 | 1116 | 2938 | 4839 | 4790 | 98.9874 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 41.1414 | 67.0732 | 29.6703 | 62.4742 | 55 | 27 | 54 | 128 | 119 | 92.9688 | |
| ndellapenna-hhga | SNP | * | map_l100_m2_e1 | homalt | 99.7857 | 99.6546 | 99.9170 | 62.4746 | 27700 | 96 | 27700 | 23 | 21 | 91.3043 | |
| ckim-gatk | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8503 | 99.8005 | 99.9001 | 62.4759 | 7005 | 14 | 7001 | 7 | 3 | 42.8571 | |
| mlin-fermikit | INDEL | I1_5 | * | hetalt | 79.4455 | 66.1635 | 99.3997 | 62.4768 | 7407 | 3788 | 7451 | 45 | 45 | 100.0000 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 38.7872 | 35.8879 | 42.1961 | 62.4776 | 1152 | 2058 | 1149 | 1574 | 1547 | 98.2846 | |
| ltrigg-rtg1 | SNP | * | map_l100_m2_e0 | homalt | 99.8182 | 99.7420 | 99.8945 | 62.4790 | 27452 | 71 | 27451 | 29 | 26 | 89.6552 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 57.9193 | 56.2153 | 59.7299 | 62.4801 | 36735 | 28612 | 56563 | 38135 | 29523 | 77.4171 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 57.9193 | 56.2153 | 59.7299 | 62.4801 | 36735 | 28612 | 56563 | 38135 | 29523 | 77.4171 | |
| ndellapenna-hhga | SNP | * | map_l100_m2_e0 | homalt | 99.7835 | 99.6512 | 99.9162 | 62.4810 | 27427 | 96 | 27427 | 23 | 21 | 91.3043 | |
| ckim-gatk | INDEL | D1_5 | * | homalt | 99.8051 | 99.9366 | 99.6739 | 62.4819 | 48895 | 31 | 48902 | 160 | 157 | 98.1250 | |
| egarrison-hhga | INDEL | I1_5 | HG002compoundhet | * | 96.1134 | 95.0631 | 97.1871 | 62.4825 | 11746 | 610 | 11747 | 340 | 264 | 77.6471 | |
| hfeng-pmm3 | SNP | ti | map_l100_m2_e1 | homalt | 99.8675 | 99.8540 | 99.8810 | 62.4833 | 18467 | 27 | 18467 | 22 | 12 | 54.5455 | |
| qzeng-custom | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.7317 | 99.7821 | 99.6812 | 62.4851 | 10075 | 22 | 10007 | 32 | 21 | 65.6250 | |