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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
75401-75450 / 86044 show all | |||||||||||||||
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 74.7354 | 78.9833 | 70.9211 | 58.2978 | 1041 | 277 | 1178 | 483 | 222 | 45.9627 | |
| ciseli-custom | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 76.6099 | 94.2733 | 64.5210 | 69.8327 | 4560 | 277 | 4701 | 2585 | 206 | 7.9691 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.6494 | 97.0713 | 98.2344 | 36.6573 | 9181 | 277 | 10015 | 180 | 172 | 95.5556 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 28.4088 | 28.0519 | 28.7749 | 80.0908 | 108 | 277 | 202 | 500 | 107 | 21.4000 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.7168 | 0.0000 | 0.0000 | 2 | 277 | 0 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | * | * | homalt | 99.6836 | 99.7787 | 99.5886 | 55.4406 | 124895 | 277 | 124903 | 516 | 501 | 97.0930 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.6119 | 95.3351 | 100.0000 | 63.4087 | 5661 | 277 | 5698 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.4735 | 88.5110 | 99.0255 | 55.9755 | 2134 | 277 | 2134 | 21 | 19 | 90.4762 | |
| ckim-vqsr | SNP | * | HG002compoundhet | homalt | 98.6617 | 97.4309 | 99.9239 | 35.4419 | 10505 | 277 | 10504 | 8 | 7 | 87.5000 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.9791 | 94.1744 | 99.9560 | 31.2217 | 4494 | 278 | 4547 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | SNP | tv | map_l150_m2_e0 | * | 98.6727 | 97.5517 | 99.8198 | 64.8483 | 11077 | 278 | 11076 | 20 | 2 | 10.0000 | |
| ltrigg-rtg2 | SNP | tv | map_l150_m2_e1 | * | 98.6899 | 97.5830 | 99.8222 | 64.8925 | 11224 | 278 | 11226 | 20 | 2 | 10.0000 | |
| eyeh-varpipe | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.9963 | 99.5003 | 96.5372 | 58.7333 | 55353 | 278 | 52773 | 1893 | 213 | 11.2520 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.3584 | 0.0000 | 0.0000 | 1 | 278 | 0 | 0 | 0 | ||
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.4072 | 95.3136 | 99.5949 | 50.5186 | 5654 | 278 | 5654 | 23 | 21 | 91.3043 | |
| rpoplin-dv42 | INDEL | I6_15 | * | het | 96.6553 | 97.2291 | 96.0883 | 56.6301 | 9755 | 278 | 9752 | 397 | 383 | 96.4736 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.8954 | 94.0176 | 99.9548 | 27.2727 | 4369 | 278 | 4422 | 2 | 2 | 100.0000 | |
| hfeng-pmm1 | SNP | * | map_l150_m2_e0 | * | 99.3518 | 99.1272 | 99.5773 | 75.1179 | 31574 | 278 | 31568 | 134 | 37 | 27.6119 | |
| hfeng-pmm1 | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4519 | 98.9956 | 99.9125 | 62.9106 | 27400 | 278 | 27391 | 24 | 10 | 41.6667 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.4016 | 97.3287 | 99.4985 | 47.5257 | 10129 | 278 | 10118 | 51 | 47 | 92.1569 | |
| hfeng-pmm3 | INDEL | D6_15 | HG002complexvar | * | 97.0065 | 94.7378 | 99.3864 | 56.7243 | 5023 | 279 | 5021 | 31 | 24 | 77.4194 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 87.6621 | 78.3888 | 99.4236 | 31.5582 | 1012 | 279 | 1035 | 6 | 5 | 83.3333 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 94.3224 | 95.8089 | 92.8813 | 84.3204 | 6378 | 279 | 6315 | 484 | 93 | 19.2149 | |
| gduggal-bwafb | INDEL | I1_5 | HG002complexvar | hetalt | 89.3217 | 83.8355 | 95.5763 | 80.3162 | 1447 | 279 | 821 | 38 | 37 | 97.3684 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 63.0031 | 47.3585 | 94.0828 | 47.0219 | 251 | 279 | 159 | 10 | 10 | 100.0000 | |
| gduggal-bwafb | SNP | ti | map_l150_m2_e0 | * | 98.7457 | 98.6398 | 98.8519 | 77.9268 | 20233 | 279 | 20233 | 235 | 69 | 29.3617 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 64.0613 | 59.9713 | 68.7500 | 40.2750 | 418 | 279 | 418 | 190 | 185 | 97.3684 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 93.8528 | 89.4478 | 98.7142 | 36.5693 | 2365 | 279 | 2380 | 31 | 29 | 93.5484 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.6655 | 98.1110 | 99.2262 | 52.5551 | 14491 | 279 | 14491 | 113 | 109 | 96.4602 | |
| ltrigg-rtg2 | INDEL | D1_5 | * | homalt | 99.7038 | 99.4298 | 99.9794 | 54.3049 | 48647 | 279 | 48525 | 10 | 9 | 90.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.6252 | 94.1534 | 99.2303 | 30.5059 | 4493 | 279 | 4512 | 35 | 32 | 91.4286 | |
| ndellapenna-hhga | INDEL | I6_15 | * | het | 97.5570 | 97.2192 | 97.8973 | 54.2636 | 9754 | 279 | 9777 | 210 | 127 | 60.4762 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 45.1608 | 33.2536 | 70.3518 | 57.5693 | 139 | 279 | 140 | 59 | 58 | 98.3051 | |
| ltrigg-rtg1 | INDEL | * | HG002complexvar | homalt | 99.4013 | 98.9677 | 99.8388 | 52.4987 | 26747 | 279 | 26629 | 43 | 32 | 74.4186 | |
| anovak-vg | INDEL | D1_5 | map_l100_m2_e1 | * | 84.5768 | 85.6111 | 83.5671 | 84.5427 | 1660 | 279 | 1668 | 328 | 123 | 37.5000 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 279 | 0 | 0 | 0 | |||
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 279 | 0 | 0 | 0 | |||
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 74.3375 | 67.6709 | 82.4611 | 55.4224 | 584 | 279 | 583 | 124 | 122 | 98.3871 | |
| gduggal-snapfb | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 279 | 0 | 0 | 0 | |||
| gduggal-snapplat | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 279 | 0 | 0 | 0 | |||
| ghariani-varprowl | SNP | * | map_l150_m0_e0 | * | 96.3674 | 97.6729 | 95.0963 | 84.3053 | 11752 | 280 | 11752 | 606 | 137 | 22.6073 | |
| ghariani-varprowl | INDEL | * | map_l100_m2_e1 | * | 90.3178 | 92.5453 | 88.1950 | 92.4782 | 3476 | 280 | 3474 | 465 | 216 | 46.4516 | |
| mlin-fermikit | INDEL | I1_5 | map_l150_m2_e1 | * | 61.8989 | 47.2693 | 89.6429 | 85.3403 | 251 | 280 | 251 | 29 | 25 | 86.2069 | |
| qzeng-custom | INDEL | I1_5 | map_l125_m2_e0 | * | 79.5482 | 67.3279 | 97.1883 | 91.0248 | 577 | 280 | 795 | 23 | 11 | 47.8261 | |
| qzeng-custom | SNP | tv | map_l250_m0_e0 | * | 73.9185 | 63.3987 | 88.6239 | 97.9721 | 485 | 280 | 483 | 62 | 45 | 72.5806 | |
| gduggal-bwafb | SNP | ti | map_l150_m2_e1 | * | 98.7513 | 98.6488 | 98.8540 | 78.0171 | 20443 | 280 | 20443 | 237 | 70 | 29.5359 | |
| gduggal-bwaplat | INDEL | * | map_l125_m0_e0 | het | 68.5268 | 52.2998 | 99.3528 | 96.8009 | 307 | 280 | 307 | 2 | 0 | 0.0000 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 93.3712 | 87.5666 | 100.0000 | 59.6774 | 1972 | 280 | 1975 | 0 | 0 | ||
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.6745 | 96.2080 | 99.1864 | 53.3595 | 7104 | 280 | 7071 | 58 | 53 | 91.3793 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.7955 | 92.0590 | 99.8481 | 42.7080 | 3246 | 280 | 3287 | 5 | 4 | 80.0000 | |