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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
8801-8850 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 59.1321 | 46.1872 | 82.1586 | 80.3718 | 745 | 868 | 746 | 162 | 24 | 14.8148 | |
| gduggal-bwaplat | SNP | * | HG002compoundhet | homalt | 95.7606 | 93.2573 | 98.4021 | 40.3893 | 10055 | 727 | 9976 | 162 | 149 | 91.9753 | |
| gduggal-bwaplat | SNP | * | map_l125_m1_e0 | * | 74.4387 | 59.4965 | 99.4030 | 86.9422 | 26968 | 18359 | 26975 | 162 | 46 | 28.3951 | |
| gduggal-bwaplat | INDEL | D1_5 | HG002compoundhet | homalt | 64.7761 | 74.5704 | 57.2559 | 81.8487 | 217 | 74 | 217 | 162 | 147 | 90.7407 | |
| gduggal-bwavard | INDEL | * | map_l125_m0_e0 | het | 86.9907 | 98.1261 | 78.1250 | 92.7637 | 576 | 11 | 575 | 161 | 28 | 17.3913 | |
| gduggal-bwafb | SNP | * | HG002complexvar | homalt | 99.8832 | 99.8222 | 99.9441 | 19.8833 | 288062 | 513 | 288090 | 161 | 137 | 85.0932 | |
| bgallagher-sentieon | SNP | ti | map_l125_m0_e0 | * | 98.9758 | 99.2086 | 98.7441 | 75.3623 | 12661 | 101 | 12659 | 161 | 31 | 19.2547 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 28.7100 | 20.4082 | 48.3974 | 46.2069 | 150 | 585 | 151 | 161 | 125 | 77.6398 | |
| anovak-vg | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 23.7087 | 15.9091 | 46.5116 | 54.5317 | 133 | 703 | 140 | 161 | 125 | 77.6398 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.7578 | 95.2969 | 96.2233 | 58.1854 | 4093 | 202 | 4102 | 161 | 85 | 52.7950 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 65.3595 | 55.1783 | 80.1480 | 73.4881 | 650 | 528 | 650 | 161 | 115 | 71.4286 | |
| gduggal-snapvard | INDEL | I1_5 | map_l125_m1_e0 | * | 90.5689 | 94.8193 | 86.6832 | 88.0250 | 787 | 43 | 1048 | 161 | 65 | 40.3727 | |
| gduggal-snapfb | SNP | tv | map_l250_m2_e0 | * | 94.8696 | 95.2811 | 94.4616 | 90.2325 | 2746 | 136 | 2746 | 161 | 55 | 34.1615 | |
| gduggal-snapplat | INDEL | * | map_l125_m1_e0 | het | 80.6812 | 75.2060 | 87.0161 | 93.7402 | 1004 | 331 | 1079 | 161 | 24 | 14.9068 | |
| gduggal-snapplat | INDEL | D1_5 | map_l100_m1_e0 | * | 85.3263 | 79.9784 | 91.4407 | 90.7363 | 1478 | 370 | 1720 | 161 | 32 | 19.8758 | |
| gduggal-snapplat | INDEL | I1_5 | map_l100_m2_e1 | * | 82.3761 | 78.0645 | 87.1917 | 92.5152 | 1089 | 306 | 1096 | 161 | 8 | 4.9689 | |
| jli-custom | SNP | * | map_l100_m0_e0 | het | 98.8927 | 98.5522 | 99.2355 | 65.8743 | 20898 | 307 | 20898 | 161 | 48 | 29.8137 | |
| jli-custom | SNP | * | map_l150_m1_e0 | * | 99.1511 | 98.8337 | 99.4706 | 71.1384 | 30252 | 357 | 30249 | 161 | 58 | 36.0248 | |
| jli-custom | SNP | * | map_l150_m2_e0 | het | 98.8511 | 98.5099 | 99.1946 | 74.6204 | 19833 | 300 | 19830 | 161 | 49 | 30.4348 | |
| jmaeng-gatk | INDEL | D1_5 | HG002compoundhet | homalt | 78.1671 | 99.6564 | 64.3016 | 87.6742 | 290 | 1 | 290 | 161 | 160 | 99.3789 | |
| ltrigg-rtg1 | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.0496 | 99.4927 | 98.6105 | 40.0631 | 11375 | 58 | 11426 | 161 | 2 | 1.2422 | |
| ndellapenna-hhga | SNP | * | map_siren | het | 99.3524 | 98.8878 | 99.8214 | 53.1990 | 89979 | 1012 | 89980 | 161 | 58 | 36.0248 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 84.4697 | 82.4873 | 86.5497 | 58.4519 | 975 | 207 | 1036 | 161 | 135 | 83.8509 | |
| qzeng-custom | SNP | tv | segdup | * | 98.3829 | 98.6521 | 98.1152 | 93.4371 | 8417 | 115 | 8381 | 161 | 27 | 16.7702 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 79.0971 | 72.2876 | 87.3228 | 83.3661 | 1106 | 424 | 1109 | 161 | 148 | 91.9255 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 79.0971 | 72.2876 | 87.3228 | 83.3661 | 1106 | 424 | 1109 | 161 | 148 | 91.9255 | |
| ckim-gatk | INDEL | * | map_l100_m2_e0 | * | 97.0660 | 98.4024 | 95.7654 | 89.0665 | 3634 | 59 | 3641 | 161 | 20 | 12.4224 | |
| ckim-gatk | INDEL | * | map_l100_m2_e1 | * | 97.0874 | 98.3759 | 95.8323 | 89.0990 | 3695 | 61 | 3702 | 161 | 20 | 12.4224 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 91.6583 | 85.8616 | 98.2945 | 30.7003 | 8994 | 1481 | 9279 | 161 | 143 | 88.8199 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.0660 | 95.3263 | 98.8704 | 48.8773 | 14094 | 691 | 14092 | 161 | 153 | 95.0311 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.9900 | 95.2557 | 98.7886 | 47.4309 | 13131 | 654 | 13129 | 161 | 155 | 96.2733 | |
| hfeng-pmm1 | SNP | * | map_l100_m1_e0 | * | 99.5814 | 99.3868 | 99.7767 | 62.8958 | 71959 | 444 | 71948 | 161 | 49 | 30.4348 | |
| ckim-vqsr | SNP | tv | map_l100_m1_e0 | het | 84.0404 | 73.2308 | 98.5936 | 85.7766 | 11290 | 4127 | 11287 | 161 | 1 | 0.6211 | |
| eyeh-varpipe | INDEL | * | map_siren | het | 96.4251 | 96.0958 | 96.7566 | 78.9179 | 4332 | 176 | 4803 | 161 | 108 | 67.0807 | |
| ckim-isaac | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2905 | 92.1704 | 96.5104 | 61.7853 | 4391 | 373 | 4425 | 160 | 47 | 29.3750 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 81.6460 | 74.6599 | 90.0744 | 85.4526 | 1317 | 447 | 1452 | 160 | 15 | 9.3750 | |
| dgrover-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.8905 | 99.9061 | 97.8953 | 39.6283 | 7445 | 7 | 7442 | 160 | 3 | 1.8750 | |
| ckim-vqsr | INDEL | D1_5 | * | homalt | 99.7969 | 99.9203 | 99.6738 | 62.4858 | 48887 | 39 | 48894 | 160 | 157 | 98.1250 | |
| mlin-fermikit | SNP | ti | segdup | het | 97.7090 | 96.7914 | 98.6442 | 84.9489 | 11644 | 386 | 11641 | 160 | 0 | 0.0000 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4714 | 99.5136 | 99.4293 | 48.5634 | 27823 | 136 | 27875 | 160 | 12 | 7.5000 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 88.1960 | 96.5132 | 81.1986 | 71.1330 | 692 | 25 | 691 | 160 | 160 | 100.0000 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m2_e1 | * | 77.5709 | 68.5921 | 89.2545 | 77.9440 | 1330 | 609 | 1329 | 160 | 138 | 86.2500 | |
| gduggal-snapfb | INDEL | D6_15 | HG002complexvar | het | 75.2635 | 62.8205 | 93.8532 | 43.4007 | 1960 | 1160 | 2443 | 160 | 143 | 89.3750 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 32.5074 | 80.0000 | 20.3980 | 59.7194 | 40 | 10 | 41 | 160 | 156 | 97.5000 | |
| gduggal-bwafb | INDEL | I6_15 | HG002compoundhet | het | 78.5751 | 65.8654 | 97.3628 | 22.2080 | 137 | 71 | 5907 | 160 | 152 | 95.0000 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 72.7179 | 89.8551 | 61.0706 | 92.0580 | 248 | 28 | 251 | 160 | 12 | 7.5000 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 78.1600 | 65.8800 | 96.0669 | 59.7785 | 3908 | 2024 | 3908 | 160 | 48 | 30.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.9180 | 97.0394 | 96.7968 | 74.8717 | 4851 | 148 | 4835 | 160 | 117 | 73.1250 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.9180 | 97.0394 | 96.7968 | 74.8717 | 4851 | 148 | 4835 | 160 | 117 | 73.1250 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.2431 | 99.2607 | 97.2461 | 57.3108 | 5639 | 42 | 5650 | 160 | 149 | 93.1250 | |