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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
46051-46100 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.1383 | 96.3446 | 100.0000 | 78.0038 | 369 | 14 | 346 | 0 | 0 | ||
| mlin-fermikit | INDEL | * | map_l100_m1_e0 | het | 74.2630 | 62.0134 | 92.5433 | 78.0056 | 1386 | 849 | 1390 | 112 | 68 | 60.7143 | |
| ltrigg-rtg2 | INDEL | D1_5 | map_l125_m2_e0 | het | 97.9502 | 96.8586 | 99.0667 | 78.0059 | 740 | 24 | 743 | 7 | 0 | 0.0000 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 28.8305 | 21.2560 | 44.7917 | 78.0069 | 88 | 326 | 86 | 106 | 102 | 96.2264 | |
| ltrigg-rtg1 | INDEL | D6_15 | map_siren | homalt | 97.6500 | 96.1538 | 99.1935 | 78.0142 | 125 | 5 | 123 | 1 | 0 | 0.0000 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 87.9887 | 87.7705 | 88.2080 | 78.0159 | 933 | 130 | 950 | 127 | 70 | 55.1181 | |
| gduggal-snapfb | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 14.6893 | 100.0000 | 7.9268 | 78.0161 | 13 | 0 | 13 | 151 | 3 | 1.9868 | |
| gduggal-snapfb | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 14.6893 | 100.0000 | 7.9268 | 78.0161 | 13 | 0 | 13 | 151 | 3 | 1.9868 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5144 | 99.6757 | 99.3536 | 78.0162 | 1537 | 5 | 1537 | 10 | 5 | 50.0000 | |
| gduggal-bwafb | SNP | ti | map_l150_m2_e1 | * | 98.7513 | 98.6488 | 98.8540 | 78.0171 | 20443 | 280 | 20443 | 237 | 70 | 29.5359 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l100_m2_e0 | het | 97.3799 | 96.2169 | 98.5714 | 78.0188 | 763 | 30 | 759 | 11 | 1 | 9.0909 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.6112 | 99.4825 | 99.7403 | 78.0188 | 769 | 4 | 768 | 2 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | tv | map_siren | het | 74.9187 | 59.9671 | 99.8022 | 78.0195 | 17156 | 11453 | 17153 | 34 | 10 | 29.4118 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 42.3423 | 57.3171 | 33.5714 | 78.0220 | 47 | 35 | 47 | 93 | 26 | 27.9570 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.5138 | 99.8915 | 99.1389 | 78.0222 | 921 | 1 | 921 | 8 | 3 | 37.5000 | |
| gduggal-snapplat | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 88.7092 | 85.8663 | 91.7468 | 78.0293 | 15328 | 2523 | 15363 | 1382 | 108 | 7.8148 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.3837 | 99.3515 | 99.4160 | 78.0297 | 1532 | 10 | 1532 | 9 | 5 | 55.5556 | |
| bgallagher-sentieon | INDEL | D16_PLUS | * | het | 97.5876 | 99.3036 | 95.9298 | 78.0298 | 3137 | 22 | 2899 | 123 | 76 | 61.7886 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 95.7576 | 91.8605 | 100.0000 | 78.0303 | 79 | 7 | 87 | 0 | 0 | ||
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 86.7925 | 95.8333 | 79.3103 | 78.0303 | 23 | 1 | 23 | 6 | 6 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D6_15 | map_l100_m2_e0 | hetalt | 93.7500 | 88.2353 | 100.0000 | 78.0303 | 60 | 8 | 58 | 0 | 0 | ||
| gduggal-snapfb | INDEL | I6_15 | map_siren | homalt | 82.8025 | 72.2222 | 97.0149 | 78.0328 | 65 | 25 | 65 | 2 | 2 | 100.0000 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 63.8406 | 59.0164 | 69.5238 | 78.0335 | 72 | 50 | 73 | 32 | 31 | 96.8750 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 98.5348 | 97.9964 | 99.0792 | 78.0340 | 538 | 11 | 538 | 5 | 4 | 80.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.0909 | 96.7581 | 99.4609 | 78.0343 | 388 | 13 | 369 | 2 | 2 | 100.0000 | |
| ckim-isaac | SNP | * | map_l150_m2_e1 | * | 70.6272 | 54.6818 | 99.7000 | 78.0346 | 17613 | 14597 | 17614 | 53 | 14 | 26.4151 | |
| mlin-fermikit | INDEL | D1_5 | map_l125_m1_e0 | homalt | 72.3589 | 71.6332 | 73.0994 | 78.0347 | 250 | 99 | 250 | 92 | 86 | 93.4783 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 97.3617 | 96.3504 | 98.3945 | 78.0353 | 396 | 15 | 429 | 7 | 7 | 100.0000 | |
| ltrigg-rtg1 | INDEL | * | map_siren | homalt | 99.1870 | 98.9077 | 99.4679 | 78.0366 | 2626 | 29 | 2617 | 14 | 10 | 71.4286 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7255 | 99.8168 | 99.6344 | 78.0409 | 545 | 1 | 545 | 2 | 2 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7250 | 99.6337 | 99.8165 | 78.0419 | 544 | 2 | 544 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7250 | 99.6337 | 99.8165 | 78.0419 | 544 | 2 | 544 | 1 | 1 | 100.0000 | |
| gduggal-bwavard | SNP | * | map_l100_m1_e0 | het | 95.2191 | 97.5462 | 93.0004 | 78.0483 | 44246 | 1113 | 43686 | 3288 | 213 | 6.4781 | |
| gduggal-snapvard | INDEL | I16_PLUS | map_l125_m1_e0 | het | 35.0877 | 22.2222 | 83.3333 | 78.0488 | 2 | 7 | 15 | 3 | 2 | 66.6667 | |
| rpoplin-dv42 | INDEL | I16_PLUS | map_l125_m1_e0 | het | 88.8889 | 88.8889 | 88.8889 | 78.0488 | 8 | 1 | 8 | 1 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.3116 | 97.6190 | 97.0060 | 78.0552 | 164 | 4 | 162 | 5 | 2 | 40.0000 | |
| anovak-vg | SNP | tv | map_l125_m2_e0 | het | 77.3239 | 91.5342 | 66.9329 | 78.0559 | 9558 | 884 | 9554 | 4720 | 1043 | 22.0975 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 81.9603 | 79.1667 | 84.9582 | 78.0562 | 304 | 80 | 305 | 54 | 43 | 79.6296 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.3716 | 99.1196 | 99.6249 | 78.0612 | 1351 | 12 | 1328 | 5 | 3 | 60.0000 | |
| gduggal-bwaplat | INDEL | * | HG002complexvar | hetalt | 79.9153 | 68.2076 | 96.4751 | 78.0617 | 2523 | 1176 | 2518 | 92 | 88 | 95.6522 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 80.8824 | 93.2203 | 71.4286 | 78.0627 | 55 | 4 | 55 | 22 | 22 | 100.0000 | |
| jlack-gatk | SNP | * | map_l100_m0_e0 | * | 95.5864 | 98.6663 | 92.6930 | 78.0628 | 32403 | 438 | 32399 | 2554 | 207 | 8.1049 | |
| gduggal-bwafb | SNP | ti | map_l150_m1_e0 | het | 98.3399 | 98.4074 | 98.2724 | 78.0641 | 12173 | 197 | 12173 | 214 | 63 | 29.4393 | |
| raldana-dualsentieon | SNP | * | map_l150_m2_e1 | het | 98.5420 | 98.7576 | 98.3273 | 78.0672 | 20110 | 253 | 20104 | 342 | 4 | 1.1696 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.1538 | 92.5926 | 100.0000 | 78.0702 | 75 | 6 | 75 | 0 | 0 | ||
| jpowers-varprowl | INDEL | I6_15 | map_l100_m1_e0 | homalt | 82.7586 | 72.7273 | 96.0000 | 78.0702 | 24 | 9 | 24 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | SNP | tv | map_l125_m2_e0 | * | 97.4321 | 98.7143 | 96.1827 | 78.0708 | 16277 | 212 | 16277 | 646 | 117 | 18.1115 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 96.1286 | 95.3020 | 96.9697 | 78.0731 | 142 | 7 | 128 | 4 | 2 | 50.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | HG002compoundhet | homalt | 8.6957 | 100.0000 | 4.5455 | 78.0731 | 3 | 0 | 3 | 63 | 59 | 93.6508 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 100.0000 | 100.0000 | 100.0000 | 78.0735 | 346 | 0 | 346 | 0 | 0 | ||