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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
62051-62100 / 86044 show all | |||||||||||||||
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.4101 | 94.7437 | 98.1362 | 57.6003 | 7967 | 442 | 10057 | 191 | 176 | 92.1466 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 96.4103 | 97.9167 | 94.9495 | 46.7742 | 188 | 4 | 188 | 10 | 9 | 90.0000 | |
| jmaeng-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.4103 | 93.0693 | 100.0000 | 93.4677 | 94 | 7 | 94 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 96.4104 | 94.8905 | 97.9798 | 71.8750 | 390 | 21 | 388 | 8 | 8 | 100.0000 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.4108 | 95.2812 | 97.5675 | 40.2387 | 23382 | 1158 | 24186 | 603 | 555 | 92.0398 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.4114 | 96.3910 | 96.4318 | 79.9786 | 1282 | 48 | 1081 | 40 | 36 | 90.0000 | |
| gduggal-bwafb | INDEL | * | map_l150_m2_e0 | * | 96.4133 | 95.3125 | 97.5398 | 89.5080 | 1342 | 66 | 1348 | 34 | 8 | 23.5294 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.4143 | 93.5567 | 99.4521 | 72.2433 | 363 | 25 | 363 | 2 | 1 | 50.0000 | |
| hfeng-pmm2 | INDEL | * | segdup | hetalt | 96.4143 | 93.0769 | 100.0000 | 94.8471 | 121 | 9 | 123 | 0 | 0 | ||
| raldana-dualsentieon | INDEL | D6_15 | map_l100_m1_e0 | het | 96.4143 | 96.0317 | 96.8000 | 86.3983 | 121 | 5 | 121 | 4 | 1 | 25.0000 | |
| rpoplin-dv42 | INDEL | * | segdup | hetalt | 96.4143 | 93.0769 | 100.0000 | 95.1464 | 121 | 9 | 121 | 0 | 0 | ||
| dgrover-gatk | INDEL | D6_15 | map_l125_m2_e1 | * | 96.4143 | 94.5312 | 98.3740 | 91.7616 | 121 | 7 | 121 | 2 | 1 | 50.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l125_m0_e0 | * | 96.4143 | 97.5806 | 95.2756 | 92.2773 | 484 | 12 | 484 | 24 | 3 | 12.5000 | |
| bgallagher-sentieon | INDEL | * | segdup | hetalt | 96.4143 | 93.0769 | 100.0000 | 94.3681 | 121 | 9 | 123 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | * | segdup | hetalt | 96.4143 | 93.0769 | 100.0000 | 94.8341 | 121 | 9 | 123 | 0 | 0 | ||
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.4144 | 93.0885 | 99.9868 | 28.9050 | 7502 | 557 | 7550 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.4144 | 93.0885 | 99.9868 | 28.9050 | 7502 | 557 | 7550 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | HG002compoundhet | hetalt | 96.4145 | 93.0772 | 100.0000 | 29.8859 | 7946 | 591 | 7986 | 0 | 0 | ||
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.4153 | 95.0558 | 97.8143 | 50.9442 | 14054 | 731 | 14052 | 314 | 309 | 98.4076 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 96.4154 | 95.9514 | 96.8839 | 75.2281 | 711 | 30 | 684 | 22 | 19 | 86.3636 | |
| asubramanian-gatk | INDEL | I1_5 | map_l100_m1_e0 | homalt | 96.4155 | 93.4363 | 99.5910 | 81.7265 | 484 | 34 | 487 | 2 | 2 | 100.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.4163 | 93.6820 | 99.3151 | 38.7290 | 1809 | 122 | 2030 | 14 | 14 | 100.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.4163 | 93.6820 | 99.3151 | 38.7290 | 1809 | 122 | 2030 | 14 | 14 | 100.0000 | |
| cchapple-custom | SNP | ti | map_l125_m2_e0 | het | 96.4167 | 97.1816 | 95.6637 | 78.2290 | 18344 | 532 | 18355 | 832 | 229 | 27.5240 | |
| gduggal-bwaplat | INDEL | D1_5 | func_cds | * | 96.4169 | 93.0818 | 100.0000 | 49.3151 | 148 | 11 | 148 | 0 | 0 | ||
| dgrover-gatk | INDEL | * | HG002complexvar | hetalt | 96.4173 | 94.5931 | 98.3131 | 68.7891 | 3499 | 200 | 3730 | 64 | 63 | 98.4375 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.4177 | 93.7063 | 99.2908 | 56.4815 | 268 | 18 | 280 | 2 | 2 | 100.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.4185 | 93.4618 | 99.5685 | 26.7894 | 6647 | 465 | 6691 | 29 | 29 | 100.0000 | |
| gduggal-bwafb | INDEL | * | HG002complexvar | * | 96.4189 | 94.4813 | 98.4377 | 54.9407 | 72692 | 4246 | 74289 | 1179 | 1015 | 86.0899 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.4197 | 94.8503 | 98.0420 | 61.5230 | 61113 | 3318 | 60987 | 1218 | 972 | 79.8030 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.4200 | 93.0876 | 100.0000 | 40.2817 | 202 | 15 | 212 | 0 | 0 | ||
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.4202 | 96.3492 | 96.4912 | 68.0265 | 607 | 23 | 605 | 22 | 7 | 31.8182 | |
| bgallagher-sentieon | INDEL | D16_PLUS | * | hetalt | 96.4203 | 93.6886 | 99.3161 | 38.7676 | 1811 | 122 | 2033 | 14 | 14 | 100.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.4212 | 93.4764 | 99.5575 | 27.4245 | 6706 | 468 | 6750 | 30 | 29 | 96.6667 | |
| gduggal-bwafb | INDEL | * | map_l150_m2_e1 | * | 96.4212 | 95.3440 | 97.5230 | 89.5147 | 1372 | 67 | 1378 | 35 | 8 | 22.8571 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 96.4218 | 98.8417 | 94.1176 | 60.2339 | 256 | 3 | 256 | 16 | 15 | 93.7500 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.4244 | 95.8506 | 97.0051 | 52.0671 | 13213 | 572 | 13215 | 408 | 385 | 94.3627 | |
| eyeh-varpipe | INDEL | * | map_siren | het | 96.4251 | 96.0958 | 96.7566 | 78.9179 | 4332 | 176 | 4803 | 161 | 108 | 67.0807 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.4252 | 93.5104 | 99.5276 | 29.6399 | 7536 | 523 | 7584 | 36 | 36 | 100.0000 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.4252 | 93.5104 | 99.5276 | 29.6399 | 7536 | 523 | 7584 | 36 | 36 | 100.0000 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 96.4258 | 95.4620 | 97.4092 | 41.9487 | 3492 | 166 | 3459 | 92 | 56 | 60.8696 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 96.4259 | 96.9186 | 95.9382 | 41.0474 | 1321 | 42 | 12117 | 513 | 483 | 94.1520 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 96.4262 | 94.1386 | 98.8277 | 32.4619 | 9797 | 610 | 9779 | 116 | 87 | 75.0000 | |
| ckim-isaac | SNP | ti | HG002complexvar | het | 96.4266 | 93.1447 | 99.9482 | 15.3403 | 293188 | 21578 | 293343 | 152 | 18 | 11.8421 | |
| jlack-gatk | SNP | ti | map_l100_m2_e1 | het | 96.4266 | 99.2506 | 93.7588 | 78.7315 | 30728 | 232 | 30721 | 2045 | 177 | 8.6553 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 96.4272 | 98.7275 | 94.2317 | 67.6240 | 1862 | 24 | 1944 | 119 | 18 | 15.1261 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 96.4276 | 94.3750 | 98.5714 | 88.7910 | 151 | 9 | 138 | 2 | 0 | 0.0000 | |
| gduggal-bwavard | SNP | * | map_l100_m1_e0 | * | 96.4277 | 97.4269 | 95.4487 | 73.9277 | 70540 | 1863 | 69564 | 3317 | 236 | 7.1149 | |
| ndellapenna-hhga | INDEL | D6_15 | map_l150_m2_e0 | homalt | 96.4286 | 96.4286 | 96.4286 | 89.5911 | 27 | 1 | 27 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | D6_15 | map_l150_m2_e1 | homalt | 96.4286 | 93.1034 | 100.0000 | 90.0369 | 27 | 2 | 27 | 0 | 0 | ||