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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
44601-44650 / 86044 show all | |||||||||||||||
| gduggal-snapvard | INDEL | D1_5 | map_l100_m2_e0 | homalt | 94.4381 | 90.9984 | 98.1481 | 75.9754 | 556 | 55 | 689 | 13 | 12 | 92.3077 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 67.8262 | 71.8519 | 64.2276 | 75.9766 | 97 | 38 | 79 | 44 | 37 | 84.0909 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.4468 | 99.0921 | 99.8040 | 75.9768 | 1528 | 14 | 1528 | 3 | 1 | 33.3333 | |
| dgrover-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4181 | 99.5505 | 99.2861 | 75.9770 | 48054 | 217 | 47844 | 344 | 262 | 76.1628 | |
| gduggal-bwafb | SNP | ti | map_l125_m2_e1 | het | 98.6133 | 98.7321 | 98.4947 | 75.9784 | 18845 | 242 | 18845 | 288 | 78 | 27.0833 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.9363 | 99.2849 | 98.5900 | 75.9853 | 19439 | 140 | 19439 | 278 | 23 | 8.2734 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.9363 | 99.2849 | 98.5900 | 75.9853 | 19439 | 140 | 19439 | 278 | 23 | 8.2734 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7912 | 100.0000 | 99.5833 | 75.9880 | 478 | 0 | 478 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7912 | 100.0000 | 99.5833 | 75.9880 | 478 | 0 | 478 | 2 | 2 | 100.0000 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6683 | 99.5308 | 99.8063 | 75.9886 | 3606 | 17 | 3606 | 7 | 5 | 71.4286 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.7061 | 99.9315 | 99.4818 | 75.9939 | 21884 | 15 | 21884 | 114 | 113 | 99.1228 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.8272 | 88.3721 | 100.0000 | 76.0000 | 76 | 10 | 102 | 0 | 0 | ||
| anovak-vg | INDEL | I16_PLUS | map_l150_m2_e0 | homalt | 33.3333 | 33.3333 | 33.3333 | 76.0000 | 1 | 2 | 2 | 4 | 3 | 75.0000 | |
| anovak-vg | INDEL | I16_PLUS | map_l150_m2_e1 | homalt | 33.3333 | 33.3333 | 33.3333 | 76.0000 | 1 | 2 | 2 | 4 | 3 | 75.0000 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 13.1980 | 7.2626 | 72.2222 | 76.0000 | 13 | 166 | 13 | 5 | 4 | 80.0000 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 72.2222 | 56.5217 | 100.0000 | 76.0000 | 13 | 10 | 6 | 0 | 0 | ||
| hfeng-pmm3 | SNP | ti | map_l125_m2_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 76.0000 | 24 | 0 | 24 | 0 | 0 | ||
| hfeng-pmm3 | SNP | ti | map_l125_m2_e1 | hetalt | 100.0000 | 100.0000 | 100.0000 | 76.0000 | 24 | 0 | 24 | 0 | 0 | ||
| hfeng-pmm2 | SNP | ti | map_l125_m2_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 76.0000 | 24 | 0 | 24 | 0 | 0 | ||
| hfeng-pmm2 | SNP | ti | map_l125_m2_e1 | hetalt | 100.0000 | 100.0000 | 100.0000 | 76.0000 | 24 | 0 | 24 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.4987 | 91.5493 | 97.6445 | 76.0021 | 455 | 42 | 456 | 11 | 11 | 100.0000 | |
| mlin-fermikit | INDEL | I1_5 | HG002compoundhet | homalt | 49.1644 | 93.9210 | 33.2972 | 76.0021 | 309 | 20 | 307 | 615 | 607 | 98.6992 | |
| rpoplin-dv42 | INDEL | * | HG002compoundhet | het | 81.4607 | 94.3576 | 71.6654 | 76.0047 | 3863 | 231 | 3804 | 1504 | 1483 | 98.6037 | |
| astatham-gatk | SNP | ti | map_l125_m2_e0 | * | 91.2512 | 84.0571 | 99.7920 | 76.0047 | 25434 | 4824 | 25430 | 53 | 29 | 54.7170 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 82.4169 | 95.5954 | 72.4316 | 76.0055 | 43689 | 2013 | 43987 | 16742 | 965 | 5.7640 | |
| ciseli-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 82.4169 | 95.5954 | 72.4316 | 76.0055 | 43689 | 2013 | 43987 | 16742 | 965 | 5.7640 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.7697 | 99.5913 | 99.9487 | 76.0057 | 3899 | 16 | 3899 | 2 | 2 | 100.0000 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.2925 | 95.9395 | 98.6842 | 76.0063 | 1205 | 51 | 1200 | 16 | 7 | 43.7500 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 94.7138 | 93.2886 | 96.1832 | 76.0073 | 139 | 10 | 126 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | D6_15 | map_siren | hetalt | 96.9072 | 94.9495 | 98.9474 | 76.0101 | 94 | 5 | 94 | 1 | 0 | 0.0000 | |
| jpowers-varprowl | SNP | tv | map_l100_m2_e0 | het | 96.9118 | 97.1668 | 96.6583 | 76.0137 | 15330 | 447 | 15330 | 530 | 100 | 18.8679 | |
| jlack-gatk | SNP | tv | map_l100_m1_e0 | * | 96.1408 | 99.1511 | 93.3080 | 76.0138 | 24293 | 208 | 24289 | 1742 | 100 | 5.7405 | |
| dgrover-gatk | INDEL | I16_PLUS | * | het | 98.6296 | 98.3076 | 98.9537 | 76.0151 | 2672 | 46 | 2648 | 28 | 9 | 32.1429 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.5568 | 97.9679 | 99.1528 | 76.0152 | 5978 | 124 | 7490 | 64 | 52 | 81.2500 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 100.0000 | 100.0000 | 100.0000 | 76.0181 | 53 | 0 | 53 | 0 | 0 | ||
| ckim-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 100.0000 | 100.0000 | 100.0000 | 76.0181 | 53 | 0 | 53 | 0 | 0 | ||
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 38.3331 | 34.4623 | 43.1834 | 76.0195 | 2381 | 4528 | 2420 | 3184 | 342 | 10.7412 | |
| eyeh-varpipe | INDEL | I6_15 | map_l100_m2_e1 | * | 76.1809 | 68.1034 | 86.4322 | 76.0241 | 79 | 37 | 172 | 27 | 25 | 92.5926 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.2248 | 98.9691 | 99.4819 | 76.0248 | 384 | 4 | 384 | 2 | 1 | 50.0000 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0909 | 98.7850 | 99.3987 | 76.0252 | 6342 | 78 | 6282 | 38 | 24 | 63.1579 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0909 | 98.7850 | 99.3987 | 76.0252 | 6342 | 78 | 6282 | 38 | 24 | 63.1579 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 91.4729 | 100.0000 | 84.2857 | 76.0274 | 59 | 0 | 59 | 11 | 11 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6970 | 99.9315 | 99.4637 | 76.0277 | 21884 | 15 | 21884 | 118 | 117 | 99.1525 | |
| hfeng-pmm1 | SNP | ti | map_l150_m2_e0 | het | 99.1156 | 98.7579 | 99.4759 | 76.0299 | 12721 | 160 | 12717 | 67 | 17 | 25.3731 | |
| hfeng-pmm1 | SNP | * | map_l150_m2_e1 | het | 99.1153 | 98.7674 | 99.4657 | 76.0302 | 20112 | 251 | 20106 | 108 | 27 | 25.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.7368 | 90.3346 | 99.5902 | 76.0314 | 243 | 26 | 243 | 1 | 0 | 0.0000 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 64.2663 | 78.7037 | 54.3046 | 76.0317 | 85 | 23 | 82 | 69 | 42 | 60.8696 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6856 | 99.9087 | 99.4636 | 76.0319 | 21879 | 20 | 21879 | 118 | 117 | 99.1525 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.1817 | 98.5900 | 99.7805 | 76.0326 | 909 | 13 | 909 | 2 | 1 | 50.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.2940 | 95.6186 | 99.0291 | 76.0326 | 371 | 17 | 408 | 4 | 3 | 75.0000 | |