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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
30701-30750 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | D16_PLUS | map_siren | het | 91.2085 | 96.1538 | 86.7470 | 95.9234 | 75 | 3 | 72 | 11 | 2 | 18.1818 | |
| ckim-dragen | INDEL | D1_5 | map_l250_m1_e0 | * | 95.0825 | 96.4912 | 93.7143 | 95.4967 | 165 | 6 | 164 | 11 | 2 | 18.1818 | |
| ckim-dragen | INDEL | D1_5 | map_l250_m2_e0 | * | 95.4265 | 96.7391 | 94.1489 | 95.7629 | 178 | 6 | 177 | 11 | 2 | 18.1818 | |
| ckim-dragen | INDEL | D1_5 | map_l250_m2_e1 | * | 95.4509 | 96.7568 | 94.1799 | 95.8498 | 179 | 6 | 178 | 11 | 2 | 18.1818 | |
| ciseli-custom | INDEL | D6_15 | map_l125_m0_e0 | het | 46.1538 | 41.3793 | 52.1739 | 96.1474 | 12 | 17 | 12 | 11 | 2 | 18.1818 | |
| ckim-gatk | INDEL | I1_5 | map_l150_m0_e0 | * | 95.8387 | 97.7273 | 94.0217 | 94.6543 | 172 | 4 | 173 | 11 | 2 | 18.1818 | |
| ckim-gatk | INDEL | D16_PLUS | map_siren | het | 91.8695 | 97.4359 | 86.9048 | 96.2700 | 76 | 2 | 73 | 11 | 2 | 18.1818 | |
| gduggal-bwafb | SNP | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 72.2892 | 71.4286 | 73.1707 | 97.3325 | 30 | 12 | 30 | 11 | 2 | 18.1818 | |
| gduggal-bwaplat | INDEL | * | map_l100_m0_e0 | * | 73.0645 | 57.9655 | 98.8004 | 94.3818 | 906 | 657 | 906 | 11 | 2 | 18.1818 | |
| gduggal-snapfb | INDEL | * | map_l100_m2_e1 | het | 92.9455 | 91.2079 | 94.7505 | 82.9512 | 2137 | 206 | 2184 | 121 | 22 | 18.1818 | |
| gduggal-bwavard | INDEL | C1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 0.0000 | 0.0000 | 62.3288 | 90.0950 | 0 | 1 | 91 | 55 | 10 | 18.1818 | |
| gduggal-bwavard | INDEL | C1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 0.0000 | 0.0000 | 55.6452 | 90.5847 | 0 | 1 | 69 | 55 | 10 | 18.1818 | |
| gduggal-bwavard | INDEL | D16_PLUS | map_l125_m2_e0 | het | 73.4694 | 90.0000 | 62.0690 | 95.9441 | 18 | 2 | 18 | 11 | 2 | 18.1818 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.4785 | 99.4671 | 99.4898 | 52.4587 | 2240 | 12 | 2145 | 11 | 2 | 18.1818 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m0_e0 | * | 90.5391 | 95.3650 | 86.1780 | 88.0700 | 823 | 40 | 823 | 132 | 24 | 18.1818 | |
| ghariani-varprowl | SNP | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 78.1609 | 80.9524 | 75.5556 | 97.2477 | 34 | 8 | 34 | 11 | 2 | 18.1818 | |
| ghariani-varprowl | SNP | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 68.9655 | 74.0741 | 64.5161 | 97.5180 | 20 | 7 | 20 | 11 | 2 | 18.1818 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.1793 | 98.7333 | 99.6293 | 74.5125 | 2962 | 38 | 2956 | 11 | 2 | 18.1818 | |
| hfeng-pmm1 | INDEL | * | map_l125_m1_e0 | * | 97.9886 | 97.0574 | 98.9377 | 85.1509 | 2045 | 62 | 2049 | 22 | 4 | 18.1818 | |
| hfeng-pmm1 | INDEL | * | map_l125_m2_e0 | * | 98.0239 | 97.0856 | 98.9805 | 86.2460 | 2132 | 64 | 2136 | 22 | 4 | 18.1818 | |
| hfeng-pmm1 | INDEL | * | map_l125_m2_e1 | * | 98.0268 | 97.0787 | 98.9936 | 86.3673 | 2160 | 65 | 2164 | 22 | 4 | 18.1818 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 50.2732 | 40.0000 | 67.6471 | 91.9622 | 24 | 36 | 23 | 11 | 2 | 18.1818 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 88.6904 | 80.7888 | 98.3051 | 73.9357 | 635 | 151 | 638 | 11 | 2 | 18.1818 | |
| gduggal-snapvard | INDEL | C1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 73.0245 | 100.0000 | 57.5107 | 93.5296 | 1 | 0 | 134 | 99 | 18 | 18.1818 | |
| gduggal-snapfb | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 62.6263 | 88.5714 | 48.4375 | 94.7840 | 31 | 4 | 31 | 33 | 6 | 18.1818 | |
| gduggal-snapvard | SNP | * | tech_badpromoters | * | 88.3476 | 84.7134 | 92.3077 | 52.4917 | 133 | 24 | 132 | 11 | 2 | 18.1818 | |
| gduggal-snapvard | SNP | * | tech_badpromoters | het | 86.4516 | 87.0130 | 85.8974 | 57.3770 | 67 | 10 | 67 | 11 | 2 | 18.1818 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 69.3518 | 70.9929 | 67.7849 | 64.5633 | 1001 | 409 | 1576 | 749 | 136 | 18.1575 | |
| ghariani-varprowl | SNP | tv | map_l125_m2_e1 | * | 97.4430 | 98.7213 | 96.1975 | 78.1381 | 16444 | 213 | 16444 | 650 | 118 | 18.1538 | |
| ghariani-varprowl | SNP | tv | map_l125_m2_e0 | * | 97.4321 | 98.7143 | 96.1827 | 78.0708 | 16277 | 212 | 16277 | 646 | 117 | 18.1115 | |
| hfeng-pmm3 | SNP | ti | map_l100_m2_e1 | * | 99.6774 | 99.5898 | 99.7651 | 64.5884 | 49282 | 203 | 49275 | 116 | 21 | 18.1034 | |
| ghariani-varprowl | SNP | tv | map_l150_m1_e0 | * | 96.9968 | 98.4146 | 95.6193 | 80.2097 | 10739 | 173 | 10739 | 492 | 89 | 18.0894 | |
| ghariani-varprowl | SNP | tv | map_l125_m0_e0 | * | 96.2771 | 98.0848 | 94.5349 | 81.3241 | 6504 | 127 | 6504 | 376 | 68 | 18.0851 | |
| gduggal-snapfb | INDEL | D1_5 | map_l100_m2_e0 | * | 96.2111 | 96.1880 | 96.2343 | 84.4528 | 1842 | 73 | 1840 | 72 | 13 | 18.0556 | |
| jli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.4405 | 99.5463 | 99.3348 | 79.5031 | 10752 | 49 | 10752 | 72 | 13 | 18.0556 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3167 | 99.5384 | 99.0960 | 53.8093 | 6685 | 31 | 6687 | 61 | 11 | 18.0328 | |
| gduggal-bwafb | SNP | tv | map_l250_m2_e1 | het | 96.7380 | 96.5903 | 96.8862 | 90.0589 | 1898 | 67 | 1898 | 61 | 11 | 18.0328 | |
| ciseli-custom | INDEL | D1_5 | map_l125_m0_e0 | het | 72.3571 | 66.6667 | 79.1096 | 93.4101 | 230 | 115 | 231 | 61 | 11 | 18.0328 | |
| eyeh-varpipe | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.0505 | 97.9987 | 92.2745 | 68.7494 | 3085 | 63 | 2783 | 233 | 42 | 18.0258 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e0 | het | 98.2005 | 98.7742 | 97.6335 | 76.4784 | 10314 | 128 | 10314 | 250 | 45 | 18.0000 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e1 | het | 98.2193 | 98.7871 | 97.6581 | 76.5519 | 10425 | 128 | 10425 | 250 | 45 | 18.0000 | |
| ltrigg-rtg1 | SNP | * | map_l150_m1_e0 | het | 98.3972 | 97.0957 | 99.7341 | 63.5971 | 18755 | 561 | 18755 | 50 | 9 | 18.0000 | |
| raldana-dualsentieon | SNP | * | HG002complexvar | het | 99.8134 | 99.6490 | 99.9784 | 18.1564 | 463863 | 1634 | 463733 | 100 | 18 | 18.0000 | |
| bgallagher-sentieon | SNP | * | map_l250_m2_e0 | het | 98.0598 | 98.7678 | 97.3619 | 90.6085 | 5130 | 64 | 5130 | 139 | 25 | 17.9856 | |
| qzeng-custom | INDEL | D16_PLUS | * | homalt | 83.8251 | 97.1040 | 73.7410 | 65.8948 | 1643 | 49 | 1640 | 584 | 105 | 17.9795 | |
| mlin-fermikit | SNP | ti | HG002complexvar | het | 98.1941 | 96.4761 | 99.9743 | 15.7268 | 303674 | 11092 | 303641 | 78 | 14 | 17.9487 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 98.6534 | 99.7468 | 97.5836 | 59.0978 | 1576 | 4 | 1575 | 39 | 7 | 17.9487 | |
| jlack-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.6565 | 98.6074 | 98.7056 | 69.5164 | 2974 | 42 | 2974 | 39 | 7 | 17.9487 | |
| hfeng-pmm2 | INDEL | * | map_l150_m2_e1 | * | 97.8966 | 98.4712 | 97.3288 | 90.4206 | 1417 | 22 | 1421 | 39 | 7 | 17.9487 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 51.8064 | 59.5808 | 45.8266 | 64.9803 | 597 | 405 | 571 | 675 | 121 | 17.9259 | |