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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
14551-14600 / 86044 show all | |||||||||||||||
| ckim-dragen | SNP | ti | map_l250_m0_e0 | * | 96.5066 | 96.7883 | 96.2264 | 93.0796 | 1326 | 44 | 1326 | 52 | 4 | 7.6923 | |
| hfeng-pmm3 | SNP | tv | map_l150_m2_e0 | het | 99.2203 | 99.1589 | 99.2819 | 76.4022 | 7191 | 61 | 7189 | 52 | 5 | 9.6154 | |
| hfeng-pmm3 | SNP | tv | map_l150_m2_e1 | het | 99.2305 | 99.1698 | 99.2913 | 76.4144 | 7287 | 61 | 7285 | 52 | 5 | 9.6154 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 95.4742 | 91.7900 | 99.4666 | 33.0334 | 9615 | 860 | 9697 | 52 | 46 | 88.4615 | |
| jlack-gatk | INDEL | * | map_l250_m1_e0 | het | 85.8491 | 95.7895 | 77.7778 | 97.3448 | 182 | 8 | 182 | 52 | 1 | 1.9231 | |
| jlack-gatk | INDEL | * | map_l250_m2_e0 | het | 87.0690 | 96.1905 | 79.5276 | 97.4716 | 202 | 8 | 202 | 52 | 1 | 1.9231 | |
| jlack-gatk | INDEL | * | map_l250_m2_e1 | het | 87.1245 | 96.2085 | 79.6078 | 97.5319 | 203 | 8 | 203 | 52 | 1 | 1.9231 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7712 | 99.7476 | 99.7949 | 55.7977 | 25295 | 64 | 25298 | 52 | 25 | 48.0769 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 97.3289 | 98.9813 | 95.7307 | 72.6231 | 1166 | 12 | 1166 | 52 | 52 | 100.0000 | |
| jlack-gatk | INDEL | I1_5 | map_l125_m2_e1 | * | 96.2945 | 98.3908 | 94.2857 | 90.2392 | 856 | 14 | 858 | 52 | 5 | 9.6154 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.2666 | 99.8474 | 98.6925 | 59.1977 | 3925 | 6 | 3925 | 52 | 1 | 1.9231 | |
| hfeng-pmm3 | SNP | ti | HG002complexvar | het | 99.8511 | 99.7192 | 99.9834 | 16.8098 | 313882 | 884 | 313832 | 52 | 10 | 19.2308 | |
| hfeng-pmm2 | SNP | tv | map_l250_m2_e0 | * | 98.3016 | 98.4039 | 98.1994 | 89.7037 | 2836 | 46 | 2836 | 52 | 7 | 13.4615 | |
| hfeng-pmm2 | SNP | tv | map_l250_m2_e1 | * | 98.3213 | 98.4225 | 98.2204 | 89.7650 | 2870 | 46 | 2870 | 52 | 7 | 13.4615 | |
| hfeng-pmm3 | INDEL | * | map_siren | * | 99.0674 | 98.8394 | 99.2964 | 80.1151 | 7324 | 86 | 7339 | 52 | 13 | 25.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | HG002compoundhet | * | 95.0514 | 92.7671 | 97.4510 | 52.1351 | 1988 | 155 | 1988 | 52 | 50 | 96.1538 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 91.4127 | 92.9323 | 89.9420 | 85.4816 | 618 | 47 | 465 | 52 | 42 | 80.7692 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.9318 | 99.4945 | 98.3755 | 50.6856 | 3149 | 16 | 3149 | 52 | 50 | 96.1538 | |
| hfeng-pmm1 | INDEL | I6_15 | * | het | 98.8608 | 98.2558 | 99.4734 | 57.1305 | 9858 | 175 | 9823 | 52 | 34 | 65.3846 | |
| hfeng-pmm1 | SNP | tv | map_l150_m1_e0 | * | 99.3066 | 99.0927 | 99.5213 | 73.8197 | 10813 | 99 | 10811 | 52 | 14 | 26.9231 | |
| hfeng-pmm1 | SNP | tv | map_l150_m2_e0 | * | 99.3292 | 99.1193 | 99.5400 | 75.2398 | 11255 | 100 | 11253 | 52 | 14 | 26.9231 | |
| hfeng-pmm1 | SNP | tv | map_l150_m2_e1 | * | 99.3334 | 99.1219 | 99.5459 | 75.2491 | 11401 | 101 | 11399 | 52 | 14 | 26.9231 | |
| hfeng-pmm1 | SNP | tv | map_siren | het | 99.6130 | 99.4093 | 99.8175 | 56.2607 | 28440 | 169 | 28435 | 52 | 14 | 26.9231 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 72.9858 | 93.9024 | 59.6899 | 69.3587 | 77 | 5 | 77 | 52 | 48 | 92.3077 | |
| mlin-fermikit | SNP | * | func_cds | homalt | 99.5356 | 99.8137 | 99.2590 | 20.0683 | 6966 | 13 | 6966 | 52 | 48 | 92.3077 | |
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.2999 | 97.0961 | 99.5339 | 37.5098 | 11101 | 332 | 11105 | 52 | 7 | 13.4615 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 93.6576 | 91.5216 | 95.8958 | 60.2572 | 1209 | 112 | 1215 | 52 | 40 | 76.9231 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.7108 | 98.7484 | 98.6731 | 78.8824 | 3866 | 49 | 3867 | 52 | 45 | 86.5385 | |
| ndellapenna-hhga | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3259 | 98.9526 | 99.7019 | 63.0961 | 17384 | 184 | 17391 | 52 | 20 | 38.4615 | |
| ndellapenna-hhga | SNP | tv | map_l100_m2_e0 | het | 99.0369 | 98.4154 | 99.6662 | 64.6823 | 15527 | 250 | 15527 | 52 | 17 | 32.6923 | |
| ndellapenna-hhga | SNP | tv | segdup | * | 99.4730 | 99.5546 | 99.3915 | 90.2986 | 8494 | 38 | 8494 | 52 | 18 | 34.6154 | |
| qzeng-custom | INDEL | * | map_l125_m0_e0 | het | 81.0999 | 72.7428 | 91.6264 | 95.2483 | 427 | 160 | 569 | 52 | 20 | 38.4615 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.6018 | 99.6636 | 99.5400 | 55.7604 | 11258 | 38 | 11253 | 52 | 41 | 78.8462 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 83.4101 | 90.0498 | 77.6824 | 80.0684 | 181 | 20 | 181 | 52 | 41 | 78.8462 | |
| raldana-dualsentieon | INDEL | * | map_l100_m1_e0 | * | 97.9681 | 97.4066 | 98.5360 | 82.3019 | 3493 | 93 | 3500 | 52 | 13 | 25.0000 | |
| qzeng-custom | INDEL | C1_5 | * | * | 82.3488 | 80.0000 | 84.8397 | 96.6709 | 8 | 2 | 291 | 52 | 5 | 9.6154 | |
| ltrigg-rtg1 | INDEL | I6_15 | * | het | 98.5293 | 97.6179 | 99.4579 | 45.4535 | 9794 | 239 | 9540 | 52 | 14 | 26.9231 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 94.1085 | 91.0009 | 97.4359 | 68.1633 | 1982 | 196 | 1976 | 52 | 27 | 51.9231 | |
| jpowers-varprowl | INDEL | D1_5 | map_l125_m2_e0 | * | 94.6208 | 93.8758 | 95.3778 | 87.2043 | 1073 | 70 | 1073 | 52 | 27 | 51.9231 | |
| ltrigg-rtg1 | INDEL | D1_5 | HG002complexvar | hetalt | 94.6417 | 92.8994 | 96.4505 | 77.3885 | 1256 | 96 | 1413 | 52 | 51 | 98.0769 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.0694 | 89.1185 | 97.3869 | 71.5714 | 1941 | 237 | 1938 | 52 | 24 | 46.1538 | |
| jli-custom | INDEL | D16_PLUS | * | het | 97.9648 | 97.7208 | 98.2100 | 73.1193 | 3087 | 72 | 2853 | 52 | 37 | 71.1538 | |
| anovak-vg | INDEL | D1_5 | map_l250_m1_e0 | het | 72.2766 | 81.9820 | 64.6259 | 95.9781 | 91 | 20 | 95 | 52 | 22 | 42.3077 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 11.3706 | 7.7670 | 21.2121 | 59.0062 | 16 | 190 | 14 | 52 | 10 | 19.2308 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 29.4118 | 42.8571 | 22.3881 | 56.2092 | 15 | 20 | 15 | 52 | 24 | 46.1538 | |
| bgallagher-sentieon | INDEL | * | HG002compoundhet | hetalt | 96.0304 | 92.5536 | 99.7785 | 50.2300 | 23305 | 1875 | 23427 | 52 | 52 | 100.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.2548 | 94.9731 | 99.6489 | 58.8526 | 14642 | 775 | 14759 | 52 | 52 | 100.0000 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 96.8842 | 99.8788 | 94.0639 | 71.6321 | 824 | 1 | 824 | 52 | 50 | 96.1538 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 96.8842 | 99.8788 | 94.0639 | 71.6321 | 824 | 1 | 824 | 52 | 50 | 96.1538 | |
| asubramanian-gatk | INDEL | I6_15 | HG002complexvar | * | 97.6558 | 96.4524 | 98.8896 | 58.1164 | 4622 | 170 | 4631 | 52 | 44 | 84.6154 | |