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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
9501-9550 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 65.0860 | 56.7347 | 76.3203 | 57.3091 | 417 | 318 | 448 | 139 | 119 | 85.6115 | |
| qzeng-custom | INDEL | I6_15 | map_l100_m2_e1 | het | 52.5108 | 77.0492 | 39.8268 | 78.2486 | 47 | 14 | 92 | 139 | 4 | 2.8777 | |
| qzeng-custom | SNP | * | map_l100_m2_e0 | homalt | 87.8998 | 78.8141 | 99.3533 | 60.6693 | 21692 | 5831 | 21356 | 139 | 133 | 95.6835 | |
| qzeng-custom | SNP | ti | map_siren | homalt | 93.0187 | 87.2719 | 99.5758 | 47.6263 | 33090 | 4826 | 32626 | 139 | 121 | 87.0504 | |
| qzeng-custom | SNP | tv | segdup | het | 97.9263 | 98.4679 | 97.3907 | 94.6360 | 5206 | 81 | 5188 | 139 | 6 | 4.3166 | |
| raldana-dualsentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 73.4719 | 85.9184 | 64.1753 | 76.0494 | 421 | 69 | 249 | 139 | 136 | 97.8417 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 50.4391 | 35.8961 | 84.7921 | 83.3242 | 677 | 1209 | 775 | 139 | 23 | 16.5468 | |
| gduggal-snapplat | INDEL | * | map_l150_m2_e0 | * | 80.2426 | 73.1534 | 88.8532 | 94.8529 | 1030 | 378 | 1108 | 139 | 20 | 14.3885 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 63.3305 | 56.2021 | 72.5296 | 71.5411 | 367 | 286 | 367 | 139 | 118 | 84.8921 | |
| ghariani-varprowl | SNP | * | func_cds | * | 99.5441 | 99.8512 | 99.2389 | 30.8362 | 18123 | 27 | 18123 | 139 | 14 | 10.0719 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.0489 | 99.3034 | 98.7958 | 56.9516 | 11404 | 80 | 11404 | 139 | 132 | 94.9640 | |
| gduggal-snapfb | INDEL | D1_5 | map_siren | * | 96.5488 | 96.9963 | 96.1054 | 82.0770 | 3423 | 106 | 3430 | 139 | 27 | 19.4245 | |
| gduggal-snapplat | INDEL | D6_15 | * | hetalt | 51.3567 | 35.1358 | 95.3989 | 60.4943 | 2872 | 5302 | 2882 | 139 | 111 | 79.8561 | |
| gduggal-snapvard | INDEL | I6_15 | * | homalt | 43.3535 | 28.2462 | 93.2020 | 23.7129 | 1762 | 4476 | 1892 | 138 | 135 | 97.8261 | |
| ltrigg-rtg1 | SNP | tv | map_siren | het | 99.1688 | 98.8255 | 99.5144 | 50.4058 | 28273 | 336 | 28278 | 138 | 6 | 4.3478 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.3772 | 92.4257 | 96.4128 | 70.4962 | 3734 | 306 | 3709 | 138 | 44 | 31.8841 | |
| jli-custom | SNP | tv | map_siren | het | 99.4790 | 99.4407 | 99.5172 | 56.5108 | 28449 | 160 | 28447 | 138 | 26 | 18.8406 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 63.0990 | 53.8182 | 76.2478 | 70.5076 | 444 | 381 | 443 | 138 | 127 | 92.0290 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 63.0990 | 53.8182 | 76.2478 | 70.5076 | 444 | 381 | 443 | 138 | 127 | 92.0290 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0981 | 99.2004 | 98.9959 | 68.2271 | 13647 | 110 | 13606 | 138 | 117 | 84.7826 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0981 | 99.2004 | 98.9959 | 68.2271 | 13647 | 110 | 13606 | 138 | 117 | 84.7826 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.2658 | 97.2995 | 97.2323 | 75.7006 | 4864 | 135 | 4848 | 138 | 105 | 76.0870 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.2658 | 97.2995 | 97.2323 | 75.7006 | 4864 | 135 | 4848 | 138 | 105 | 76.0870 | |
| egarrison-hhga | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 79.2993 | 66.3164 | 98.6030 | 66.3016 | 10224 | 5193 | 9740 | 138 | 125 | 90.5797 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 81.1064 | 76.2066 | 86.6795 | 41.5020 | 900 | 281 | 898 | 138 | 138 | 100.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 56.7944 | 80.4054 | 43.9024 | 68.0934 | 119 | 29 | 108 | 138 | 138 | 100.0000 | |
| rpoplin-dv42 | SNP | ti | map_l100_m2_e1 | het | 99.3494 | 99.1473 | 99.5523 | 65.6527 | 30696 | 264 | 30688 | 138 | 83 | 60.1449 | |
| raldana-dualsentieon | SNP | * | map_l250_m1_e0 | * | 98.0609 | 98.0338 | 98.0881 | 87.5648 | 7080 | 142 | 7080 | 138 | 6 | 4.3478 | |
| raldana-dualsentieon | SNP | * | map_l250_m2_e1 | het | 97.5147 | 97.6444 | 97.3854 | 89.4825 | 5140 | 124 | 5140 | 138 | 3 | 2.1739 | |
| raldana-dualsentieon | SNP | tv | map_l125_m2_e1 | het | 98.8982 | 99.0998 | 98.6974 | 74.5288 | 10458 | 95 | 10456 | 138 | 1 | 0.7246 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 92.2757 | 91.7744 | 92.7824 | 61.6372 | 1774 | 159 | 1774 | 138 | 138 | 100.0000 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.6110 | 96.3981 | 98.8550 | 60.6748 | 12070 | 451 | 11914 | 138 | 125 | 90.5797 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.1803 | 98.5845 | 99.7833 | 71.8915 | 63519 | 912 | 63530 | 138 | 117 | 84.7826 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.9984 | 98.8832 | 99.1137 | 59.5275 | 15584 | 176 | 15433 | 138 | 107 | 77.5362 | |
| hfeng-pmm3 | INDEL | I1_5 | * | homalt | 99.7866 | 99.8014 | 99.7717 | 52.1729 | 60308 | 120 | 60313 | 138 | 134 | 97.1014 | |
| hfeng-pmm3 | SNP | * | map_l125_m1_e0 | het | 99.4129 | 99.3132 | 99.5129 | 70.9946 | 28197 | 195 | 28191 | 138 | 13 | 9.4203 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 79.0601 | 66.9823 | 96.4515 | 82.5174 | 3749 | 1848 | 3751 | 138 | 63 | 45.6522 | |
| ndellapenna-hhga | SNP | * | map_l100_m2_e0 | * | 99.3385 | 98.8697 | 99.8117 | 63.7221 | 73128 | 836 | 73130 | 138 | 63 | 45.6522 | |
| cchapple-custom | INDEL | D16_PLUS | HG002compoundhet | * | 93.0802 | 91.6275 | 94.5797 | 31.0588 | 2145 | 196 | 2408 | 138 | 135 | 97.8261 | |
| ciseli-custom | SNP | tv | lowcmp_SimpleRepeat_quadTR_51to200 | * | 35.8093 | 88.0952 | 22.4719 | 78.2396 | 37 | 5 | 40 | 138 | 3 | 2.1739 | |
| ciseli-custom | INDEL | C6_15 | * | homalt | 0.0000 | 0.0000 | 18.3432 | 95.1255 | 0 | 0 | 31 | 138 | 44 | 31.8841 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 61.8907 | 65.6250 | 58.5586 | 70.8916 | 189 | 99 | 195 | 138 | 60 | 43.4783 | |
| asubramanian-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 97.6630 | 98.1948 | 97.1369 | 68.1953 | 4678 | 86 | 4682 | 138 | 8 | 5.7971 | |
| asubramanian-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.5247 | 98.9580 | 96.1323 | 63.1557 | 3419 | 36 | 3430 | 138 | 1 | 0.7246 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.5983 | 99.6119 | 99.5848 | 74.9525 | 33107 | 129 | 33101 | 138 | 106 | 76.8116 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 85.3437 | 83.1499 | 87.6565 | 44.9532 | 982 | 199 | 980 | 138 | 137 | 99.2754 | |
| asubramanian-gatk | INDEL | * | map_siren | * | 93.9319 | 90.2024 | 97.9830 | 94.1412 | 6684 | 726 | 6704 | 138 | 23 | 16.6667 | |
| anovak-vg | INDEL | D16_PLUS | HG002complexvar | het | 65.7371 | 54.8329 | 82.0546 | 48.1457 | 607 | 500 | 631 | 138 | 95 | 68.8406 | |
| astatham-gatk | SNP | * | map_siren | * | 93.7139 | 88.2540 | 99.8939 | 58.6796 | 129052 | 17176 | 129029 | 137 | 67 | 48.9051 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 77.8716 | 90.2041 | 68.5057 | 80.6495 | 442 | 48 | 298 | 137 | 123 | 89.7810 | |