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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
40101-40150 / 86044 show all | |||||||||||||||
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 77.1804 | 63.0915 | 99.3707 | 35.9250 | 8853 | 5179 | 9000 | 57 | 56 | 98.2456 | |
| qzeng-custom | INDEL | I1_5 | map_l150_m2_e0 | het | 76.2838 | 63.1068 | 96.4158 | 95.2136 | 195 | 114 | 269 | 10 | 6 | 60.0000 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 76.0853 | 63.1134 | 95.7692 | 72.6027 | 746 | 436 | 747 | 33 | 30 | 90.9091 | |
| ckim-gatk | SNP | ti | map_l150_m0_e0 | het | 76.3401 | 63.1156 | 96.5755 | 93.3356 | 3217 | 1880 | 3215 | 114 | 18 | 15.7895 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 77.4032 | 63.1365 | 100.0000 | 29.1489 | 310 | 181 | 333 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 76.9656 | 63.1429 | 98.5366 | 46.7532 | 221 | 129 | 202 | 3 | 1 | 33.3333 | |
| ciseli-custom | INDEL | D16_PLUS | * | het | 73.2078 | 63.1529 | 87.0708 | 54.9379 | 1995 | 1164 | 2054 | 305 | 262 | 85.9016 | |
| anovak-vg | INDEL | I1_5 | map_l250_m2_e1 | * | 59.7641 | 63.1579 | 56.7164 | 96.7476 | 72 | 42 | 76 | 58 | 33 | 56.8966 | |
| anovak-vg | INDEL | I16_PLUS | segdup | homalt | 60.0000 | 63.1579 | 57.1429 | 87.7907 | 12 | 7 | 12 | 9 | 5 | 55.5556 | |
| gduggal-bwaplat | INDEL | D1_5 | tech_badpromoters | * | 77.4194 | 63.1579 | 100.0000 | 62.5000 | 12 | 7 | 12 | 0 | 0 | ||
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 49.2114 | 63.1579 | 40.3101 | 83.2031 | 60 | 35 | 52 | 77 | 41 | 53.2468 | |
| ndellapenna-hhga | INDEL | D6_15 | map_l125_m1_e0 | hetalt | 77.4194 | 63.1579 | 100.0000 | 90.1408 | 12 | 7 | 7 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | D6_15 | map_l125_m2_e0 | hetalt | 77.4194 | 63.1579 | 100.0000 | 90.7895 | 12 | 7 | 7 | 0 | 0 | ||
| mlin-fermikit | INDEL | I1_5 | map_l125_m2_e0 | hetalt | 77.4194 | 63.1579 | 100.0000 | 89.6552 | 12 | 7 | 12 | 0 | 0 | ||
| mlin-fermikit | INDEL | I1_5 | map_l125_m2_e1 | hetalt | 77.4194 | 63.1579 | 100.0000 | 89.9160 | 12 | 7 | 12 | 0 | 0 | ||
| ckim-isaac | SNP | * | map_l125_m2_e1 | het | 77.3202 | 63.1579 | 99.6699 | 75.2966 | 18720 | 10920 | 18722 | 62 | 10 | 16.1290 | |
| gduggal-snapvard | INDEL | D1_5 | tech_badpromoters | * | 63.5213 | 63.1579 | 63.8889 | 58.1395 | 12 | 7 | 23 | 13 | 10 | 76.9231 | |
| ckim-isaac | SNP | * | map_l100_m0_e0 | het | 77.3393 | 63.1643 | 99.7172 | 71.7888 | 13394 | 7811 | 13397 | 38 | 6 | 15.7895 | |
| ckim-isaac | INDEL | D1_5 | map_l150_m2_e0 | * | 76.9968 | 63.1717 | 98.5685 | 90.5306 | 482 | 281 | 482 | 7 | 3 | 42.8571 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 77.3563 | 63.1748 | 99.7477 | 25.6850 | 5114 | 2981 | 5140 | 13 | 13 | 100.0000 | |
| jmaeng-gatk | SNP | * | map_l125_m2_e1 | homalt | 77.4376 | 63.1930 | 99.9729 | 75.4660 | 11079 | 6453 | 11079 | 3 | 3 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 77.1180 | 63.2035 | 98.8889 | 37.9310 | 292 | 170 | 267 | 3 | 3 | 100.0000 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 70.1834 | 63.2184 | 78.8732 | 73.6059 | 55 | 32 | 56 | 15 | 14 | 93.3333 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 77.4004 | 63.2326 | 99.7503 | 28.0442 | 5168 | 3005 | 5193 | 13 | 13 | 100.0000 | |
| gduggal-bwaplat | INDEL | D6_15 | map_l125_m1_e0 | * | 77.4869 | 63.2479 | 100.0000 | 95.7544 | 74 | 43 | 74 | 0 | 0 | ||
| ckim-isaac | INDEL | I1_5 | map_l125_m2_e1 | homalt | 77.2242 | 63.2653 | 99.0868 | 80.8734 | 217 | 126 | 217 | 2 | 0 | 0.0000 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 76.3171 | 63.2653 | 96.1538 | 23.5294 | 31 | 18 | 25 | 1 | 0 | 0.0000 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 75.6674 | 63.2653 | 94.1176 | 80.8989 | 31 | 18 | 32 | 2 | 2 | 100.0000 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 75.6674 | 63.2653 | 94.1176 | 81.0056 | 31 | 18 | 32 | 2 | 2 | 100.0000 | |
| gduggal-bwaplat | INDEL | D6_15 | map_l125_m2_e1 | * | 77.5120 | 63.2812 | 100.0000 | 95.9008 | 81 | 47 | 81 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | D1_5 | map_l100_m0_e0 | het | 77.0340 | 63.2826 | 98.4211 | 94.5205 | 374 | 217 | 374 | 6 | 1 | 16.6667 | |
| gduggal-bwaplat | INDEL | I16_PLUS | HG002complexvar | hetalt | 77.0889 | 63.2836 | 98.5981 | 68.1548 | 212 | 123 | 211 | 3 | 3 | 100.0000 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 75.0708 | 63.2962 | 92.2274 | 85.6453 | 795 | 461 | 795 | 67 | 11 | 16.4179 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 67.7487 | 63.3008 | 72.8688 | 42.9423 | 7015 | 4067 | 6975 | 2597 | 2576 | 99.1914 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 63.7790 | 63.3136 | 64.2512 | 66.5049 | 107 | 62 | 133 | 74 | 74 | 100.0000 | |
| gduggal-snapvard | INDEL | D6_15 | HG002compoundhet | het | 67.0812 | 63.3178 | 71.3203 | 33.1905 | 542 | 314 | 4894 | 1968 | 1718 | 87.2967 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 76.6987 | 63.3222 | 97.2403 | 40.8261 | 568 | 329 | 599 | 17 | 14 | 82.3529 | |
| gduggal-snapfb | INDEL | D6_15 | HG002compoundhet | * | 72.3856 | 63.3263 | 84.4695 | 30.0529 | 5719 | 3312 | 6592 | 1212 | 1198 | 98.8449 | |
| eyeh-varpipe | INDEL | I6_15 | map_l125_m1_e0 | het | 72.5049 | 63.3333 | 84.7826 | 81.8182 | 19 | 11 | 39 | 7 | 5 | 71.4286 | |
| eyeh-varpipe | INDEL | I6_15 | map_l125_m2_e0 | het | 72.5049 | 63.3333 | 84.7826 | 83.2117 | 19 | 11 | 39 | 7 | 5 | 71.4286 | |
| eyeh-varpipe | INDEL | I6_15 | map_l125_m2_e1 | het | 72.5049 | 63.3333 | 84.7826 | 83.5125 | 19 | 11 | 39 | 7 | 5 | 71.4286 | |
| ciseli-custom | SNP | * | map_l125_m1_e0 | hetalt | 71.6981 | 63.3333 | 82.6087 | 75.5319 | 19 | 11 | 19 | 4 | 3 | 75.0000 | |
| ciseli-custom | SNP | * | map_l125_m2_e0 | hetalt | 71.6981 | 63.3333 | 82.6087 | 79.2793 | 19 | 11 | 19 | 4 | 3 | 75.0000 | |
| ciseli-custom | SNP | * | map_l125_m2_e1 | hetalt | 71.6981 | 63.3333 | 82.6087 | 79.6460 | 19 | 11 | 19 | 4 | 3 | 75.0000 | |
| cchapple-custom | INDEL | D16_PLUS | map_l100_m2_e1 | hetalt | 0.0000 | 63.3333 | 0.0000 | 0.0000 | 19 | 11 | 0 | 0 | 0 | ||
| ciseli-custom | SNP | tv | map_l125_m1_e0 | hetalt | 71.6981 | 63.3333 | 82.6087 | 75.5319 | 19 | 11 | 19 | 4 | 3 | 75.0000 | |
| ciseli-custom | SNP | tv | map_l125_m2_e0 | hetalt | 71.6981 | 63.3333 | 82.6087 | 79.2793 | 19 | 11 | 19 | 4 | 3 | 75.0000 | |
| ciseli-custom | SNP | tv | map_l125_m2_e1 | hetalt | 71.6981 | 63.3333 | 82.6087 | 79.6460 | 19 | 11 | 19 | 4 | 3 | 75.0000 | |
| jmaeng-gatk | SNP | * | map_l125_m1_e0 | hetalt | 77.5510 | 63.3333 | 100.0000 | 91.8103 | 19 | 11 | 19 | 0 | 0 | ||
| jmaeng-gatk | SNP | * | map_l125_m2_e0 | hetalt | 77.5510 | 63.3333 | 100.0000 | 93.0909 | 19 | 11 | 19 | 0 | 0 | ||