PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
67301-67350 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.6910 | 99.5997 | 97.7987 | 75.1563 | 1244 | 5 | 1244 | 28 | 22 | 78.5714 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.6910 | 99.5997 | 97.7987 | 75.1563 | 1244 | 5 | 1244 | 28 | 22 | 78.5714 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.9438 | 95.5133 | 98.4177 | 45.4467 | 1256 | 59 | 1244 | 20 | 12 | 60.0000 | |
| jlack-gatk | INDEL | * | map_l100_m2_e0 | homalt | 98.7694 | 98.6519 | 98.8871 | 83.9295 | 1244 | 17 | 1244 | 14 | 6 | 42.8571 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.8086 | 99.5997 | 98.0299 | 75.0492 | 1244 | 5 | 1244 | 25 | 20 | 80.0000 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.8086 | 99.5997 | 98.0299 | 75.0492 | 1244 | 5 | 1244 | 25 | 20 | 80.0000 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.6910 | 99.5997 | 97.7987 | 75.1563 | 1244 | 5 | 1244 | 28 | 22 | 78.5714 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.6910 | 99.5997 | 97.7987 | 75.1563 | 1244 | 5 | 1244 | 28 | 22 | 78.5714 | |
| eyeh-varpipe | INDEL | I1_5 | HG002complexvar | hetalt | 71.6240 | 56.8366 | 96.8118 | 75.7679 | 981 | 745 | 1245 | 41 | 39 | 95.1220 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 59.0350 | 46.7546 | 80.0643 | 63.0729 | 1311 | 1493 | 1245 | 310 | 228 | 73.5484 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m2_e0 | het | 98.6907 | 98.8854 | 98.4968 | 85.5954 | 1242 | 14 | 1245 | 19 | 3 | 15.7895 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 82.8565 | 74.9009 | 92.7029 | 85.1241 | 1134 | 380 | 1245 | 98 | 12 | 12.2449 | |
| raldana-dualsentieon | INDEL | D1_5 | map_l100_m2_e1 | het | 98.3776 | 97.9495 | 98.8095 | 82.0257 | 1242 | 26 | 1245 | 15 | 3 | 20.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.4036 | 94.8289 | 98.0315 | 47.7581 | 1247 | 68 | 1245 | 25 | 21 | 84.0000 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m1_e0 | * | 76.7469 | 67.5325 | 88.8730 | 76.4647 | 1248 | 600 | 1246 | 156 | 136 | 87.1795 | |
| raldana-dualsentieon | INDEL | * | map_l100_m2_e0 | homalt | 98.9674 | 98.8105 | 99.1249 | 82.9559 | 1246 | 15 | 1246 | 11 | 5 | 45.4545 | |
| jmaeng-gatk | INDEL | * | map_l100_m2_e0 | homalt | 98.8497 | 98.8105 | 98.8889 | 84.7844 | 1246 | 15 | 1246 | 14 | 7 | 50.0000 | |
| ltrigg-rtg1 | INDEL | * | map_l100_m2_e0 | homalt | 99.0050 | 98.5726 | 99.4413 | 82.1306 | 1243 | 18 | 1246 | 7 | 4 | 57.1429 | |
| jpowers-varprowl | INDEL | * | map_l125_m1_e0 | het | 92.8465 | 93.3333 | 92.3647 | 89.2132 | 1246 | 89 | 1246 | 103 | 73 | 70.8738 | |
| gduggal-bwafb | INDEL | D6_15 | HG002compoundhet | hetalt | 91.1254 | 84.6645 | 98.6540 | 40.8708 | 6901 | 1250 | 1246 | 17 | 17 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 93.1937 | 87.3160 | 99.9198 | 34.2646 | 1246 | 181 | 1246 | 1 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m2_e0 | het | 93.5776 | 98.9650 | 88.7464 | 88.5144 | 1243 | 13 | 1246 | 158 | 10 | 6.3291 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l100_m2_e0 | het | 99.0064 | 99.0446 | 98.9683 | 81.1940 | 1244 | 12 | 1247 | 13 | 2 | 15.3846 | |
| rpoplin-dv42 | INDEL | * | map_l100_m2_e0 | homalt | 98.9290 | 98.8898 | 98.9683 | 83.3597 | 1247 | 14 | 1247 | 13 | 8 | 61.5385 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 89.8601 | 93.0301 | 86.8990 | 65.5793 | 1268 | 95 | 1247 | 188 | 182 | 96.8085 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 83.2079 | 85.6274 | 80.9215 | 46.7151 | 1126 | 189 | 1247 | 294 | 107 | 36.3946 | |
| ltrigg-rtg2 | SNP | ti | map_l250_m0_e0 | * | 95.0820 | 91.0219 | 99.5211 | 84.7102 | 1247 | 123 | 1247 | 6 | 3 | 50.0000 | |
| ckim-gatk | INDEL | D1_5 | map_l100_m2_e0 | het | 96.1099 | 99.1242 | 93.2735 | 89.2977 | 1245 | 11 | 1248 | 90 | 6 | 6.6667 | |
| cchapple-custom | INDEL | D1_5 | map_l100_m2_e0 | het | 96.0894 | 97.5318 | 94.6889 | 83.3900 | 1225 | 31 | 1248 | 70 | 7 | 10.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l100_m2_e0 | het | 98.4217 | 99.1242 | 97.7291 | 84.1426 | 1245 | 11 | 1248 | 29 | 2 | 6.8966 | |
| astatham-gatk | INDEL | * | map_l125_m1_e0 | het | 95.1476 | 93.1835 | 97.1963 | 89.1710 | 1244 | 91 | 1248 | 36 | 5 | 13.8889 | |
| egarrison-hhga | INDEL | D1_5 | map_l100_m2_e1 | het | 98.0355 | 98.3438 | 97.7291 | 83.2875 | 1247 | 21 | 1248 | 29 | 8 | 27.5862 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 85.9953 | 87.2932 | 84.7354 | 73.4127 | 1161 | 169 | 1249 | 225 | 212 | 94.2222 | |
| cchapple-custom | INDEL | * | map_l100_m2_e1 | homalt | 98.1532 | 97.5020 | 98.8133 | 82.2920 | 1249 | 32 | 1249 | 15 | 11 | 73.3333 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l100_m2_e1 | het | 98.4607 | 98.2650 | 98.6572 | 83.2006 | 1246 | 22 | 1249 | 17 | 4 | 23.5294 | |
| jpowers-varprowl | INDEL | I1_5 | map_l100_m2_e0 | * | 93.8073 | 91.3743 | 96.3735 | 84.4642 | 1250 | 118 | 1249 | 47 | 34 | 72.3404 | |
| gduggal-snapvard | INDEL | * | map_l125_m0_e0 | * | 84.1360 | 92.1769 | 77.3854 | 90.1890 | 813 | 69 | 1249 | 365 | 97 | 26.5753 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l100_m2_e0 | het | 98.5784 | 99.2038 | 97.9608 | 84.7707 | 1246 | 10 | 1249 | 26 | 4 | 15.3846 | |
| gduggal-bwafb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 91.6247 | 97.6285 | 86.3165 | 88.5095 | 1235 | 30 | 1249 | 198 | 31 | 15.6566 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.8631 | 95.1331 | 98.6572 | 48.4108 | 1251 | 64 | 1249 | 17 | 12 | 70.5882 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.9007 | 95.1331 | 98.7352 | 48.1982 | 1251 | 64 | 1249 | 16 | 11 | 68.7500 | |
| dgrover-gatk | INDEL | * | map_l100_m2_e0 | homalt | 99.0099 | 99.1277 | 98.8924 | 84.9649 | 1250 | 11 | 1250 | 14 | 6 | 42.8571 | |
| asubramanian-gatk | INDEL | I16_PLUS | HG002complexvar | * | 97.0837 | 95.3400 | 98.8924 | 68.3287 | 1248 | 61 | 1250 | 14 | 14 | 100.0000 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.6982 | 98.8933 | 98.5039 | 87.7567 | 1251 | 14 | 1251 | 19 | 13 | 68.4211 | |
| jli-custom | INDEL | * | map_l100_m2_e0 | homalt | 99.1284 | 99.2070 | 99.0499 | 83.3333 | 1251 | 10 | 1251 | 12 | 6 | 50.0000 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 31.1683 | 21.1733 | 59.0373 | 57.3384 | 1256 | 4676 | 1251 | 868 | 834 | 96.0829 | |
| ltrigg-rtg1 | INDEL | * | map_l125_m1_e0 | het | 96.1010 | 93.1835 | 99.2070 | 77.7758 | 1244 | 91 | 1251 | 10 | 0 | 0.0000 | |
| ckim-gatk | INDEL | * | map_l100_m2_e0 | homalt | 99.1677 | 99.2070 | 99.1284 | 85.1721 | 1251 | 10 | 1251 | 11 | 6 | 54.5455 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 86.1301 | 82.0915 | 90.5865 | 80.5712 | 1256 | 274 | 1251 | 130 | 79 | 60.7692 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 86.1301 | 82.0915 | 90.5865 | 80.5712 | 1256 | 274 | 1251 | 130 | 79 | 60.7692 | |