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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
25051-25100 / 86044 show all | |||||||||||||||
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.1639 | 98.4142 | 99.9251 | 72.5328 | 5337 | 86 | 5337 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.5496 | 99.5667 | 99.5326 | 76.5043 | 2987 | 13 | 2981 | 14 | 4 | 28.5714 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 87.7194 | 78.3546 | 99.6265 | 31.7400 | 981 | 271 | 1067 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8508 | 99.7870 | 99.9147 | 58.6642 | 16394 | 35 | 16393 | 14 | 4 | 28.5714 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9071 | 100.0000 | 99.8145 | 47.6826 | 2152 | 0 | 2152 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | * | map_l100_m0_e0 | het | 97.5662 | 98.0411 | 97.0958 | 88.5957 | 1001 | 20 | 1003 | 30 | 4 | 13.3333 | |
| dgrover-gatk | INDEL | * | map_l125_m0_e0 | homalt | 97.8873 | 97.8873 | 97.8873 | 88.7703 | 278 | 6 | 278 | 6 | 4 | 66.6667 | |
| dgrover-gatk | INDEL | * | map_l125_m1_e0 | het | 97.9822 | 98.0524 | 97.9120 | 89.0949 | 1309 | 26 | 1313 | 28 | 4 | 14.2857 | |
| dgrover-gatk | INDEL | * | map_l125_m1_e0 | homalt | 98.9747 | 98.9071 | 99.0424 | 86.2723 | 724 | 8 | 724 | 7 | 4 | 57.1429 | |
| dgrover-gatk | INDEL | * | map_l125_m2_e0 | het | 98.0266 | 98.0590 | 97.9943 | 89.7744 | 1364 | 27 | 1368 | 28 | 4 | 14.2857 | |
| dgrover-gatk | INDEL | * | map_l125_m2_e0 | homalt | 98.8867 | 98.9515 | 98.8220 | 87.0968 | 755 | 8 | 755 | 9 | 4 | 44.4444 | |
| dgrover-gatk | INDEL | * | map_l125_m2_e1 | het | 98.0504 | 98.0824 | 98.0184 | 89.8484 | 1381 | 27 | 1385 | 28 | 4 | 14.2857 | |
| dgrover-gatk | INDEL | * | map_l125_m2_e1 | homalt | 98.9025 | 98.9664 | 98.8387 | 87.1943 | 766 | 8 | 766 | 9 | 4 | 44.4444 | |
| dgrover-gatk | INDEL | * | map_l150_m0_e0 | * | 96.9996 | 97.2763 | 96.7245 | 93.1872 | 500 | 14 | 502 | 17 | 4 | 23.5294 | |
| dgrover-gatk | INDEL | * | map_l150_m2_e1 | homalt | 98.4741 | 98.3740 | 98.5743 | 89.6632 | 484 | 8 | 484 | 7 | 4 | 57.1429 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002complexvar | homalt | 98.7952 | 99.3080 | 98.2877 | 76.1047 | 287 | 2 | 287 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.8851 | 96.3010 | 99.5221 | 33.9384 | 755 | 29 | 833 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | map_l100_m1_e0 | * | 86.8132 | 90.8046 | 83.1579 | 94.5371 | 79 | 8 | 79 | 16 | 4 | 25.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | map_l100_m1_e0 | het | 85.7754 | 93.4783 | 79.2453 | 95.6699 | 43 | 3 | 42 | 11 | 4 | 36.3636 | |
| dgrover-gatk | INDEL | D16_PLUS | map_l100_m2_e0 | * | 86.7725 | 91.1111 | 82.8283 | 95.1111 | 82 | 8 | 82 | 17 | 4 | 23.5294 | |
| dgrover-gatk | INDEL | D16_PLUS | map_l100_m2_e0 | het | 85.2611 | 93.7500 | 78.1818 | 96.1295 | 45 | 3 | 43 | 12 | 4 | 33.3333 | |
| dgrover-gatk | INDEL | D16_PLUS | map_l100_m2_e1 | * | 87.1287 | 90.7216 | 83.8095 | 94.9324 | 88 | 9 | 88 | 17 | 4 | 23.5294 | |
| dgrover-gatk | INDEL | D16_PLUS | map_l100_m2_e1 | het | 86.0819 | 94.1176 | 79.3103 | 96.0137 | 48 | 3 | 46 | 12 | 4 | 33.3333 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.1693 | 98.6207 | 97.7221 | 69.8074 | 429 | 6 | 429 | 10 | 4 | 40.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8747 | 99.8104 | 99.9390 | 55.0186 | 14742 | 28 | 14744 | 9 | 4 | 44.4444 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.9009 | 96.6154 | 99.2212 | 23.1138 | 628 | 22 | 637 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m0_e0 | * | 98.1515 | 98.3778 | 97.9263 | 86.5655 | 849 | 14 | 850 | 18 | 4 | 22.2222 | |
| dgrover-gatk | INDEL | D1_5 | map_l125_m1_e0 | * | 98.5322 | 98.6213 | 98.4432 | 87.6162 | 1073 | 15 | 1075 | 17 | 4 | 23.5294 | |
| dgrover-gatk | INDEL | D1_5 | map_l125_m2_e0 | * | 98.6027 | 98.6877 | 98.5179 | 88.1508 | 1128 | 15 | 1130 | 17 | 4 | 23.5294 | |
| dgrover-gatk | INDEL | D1_5 | map_l125_m2_e1 | * | 98.6196 | 98.7035 | 98.5357 | 88.1988 | 1142 | 15 | 1144 | 17 | 4 | 23.5294 | |
| dgrover-gatk | INDEL | D1_5 | map_l150_m2_e1 | * | 98.2053 | 98.3290 | 98.0818 | 90.2929 | 765 | 13 | 767 | 15 | 4 | 26.6667 | |
| dgrover-gatk | INDEL | D1_5 | map_siren | homalt | 99.5720 | 99.4863 | 99.6578 | 81.5178 | 1162 | 6 | 1165 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.4553 | 99.3353 | 99.5755 | 60.7194 | 1644 | 11 | 1642 | 7 | 4 | 57.1429 | |
| dgrover-gatk | INDEL | D6_15 | segdup | * | 96.3351 | 96.3351 | 96.3351 | 93.8821 | 184 | 7 | 184 | 7 | 4 | 57.1429 | |
| dgrover-gatk | INDEL | D6_15 | segdup | homalt | 96.1538 | 100.0000 | 92.5926 | 92.4051 | 50 | 0 | 50 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.6602 | 96.7890 | 98.5472 | 85.8707 | 422 | 14 | 407 | 6 | 4 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | * | hetalt | 97.2805 | 94.7387 | 99.9625 | 62.4322 | 10606 | 589 | 10669 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | HG002complexvar | hetalt | 98.0896 | 96.4658 | 99.7691 | 70.7729 | 1665 | 61 | 1728 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m1_e0 | * | 98.9542 | 98.8051 | 99.1038 | 84.0367 | 1323 | 16 | 1327 | 12 | 4 | 33.3333 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m1_e0 | homalt | 99.4231 | 99.8069 | 99.0421 | 80.9489 | 517 | 1 | 517 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m2_e0 | * | 98.9764 | 98.8304 | 99.1228 | 85.1466 | 1352 | 16 | 1356 | 12 | 4 | 33.3333 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m2_e0 | homalt | 99.4371 | 99.8117 | 99.0654 | 82.2730 | 530 | 1 | 530 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m2_e1 | * | 98.9962 | 98.8530 | 99.1398 | 85.2131 | 1379 | 16 | 1383 | 12 | 4 | 33.3333 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.4465 | 99.8148 | 99.0809 | 82.3434 | 539 | 1 | 539 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_siren | homalt | 99.6298 | 99.7525 | 99.5074 | 78.6951 | 1209 | 3 | 1212 | 6 | 4 | 66.6667 | |
| dgrover-gatk | INDEL | I6_15 | * | hetalt | 96.6039 | 93.4744 | 99.9502 | 38.7907 | 7993 | 558 | 8034 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | I6_15 | HG002complexvar | het | 99.4230 | 99.0658 | 99.7827 | 59.6952 | 2333 | 22 | 2296 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | I6_15 | map_siren | * | 97.1901 | 96.3934 | 98.0000 | 85.1852 | 294 | 11 | 294 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.7836 | 97.1503 | 98.4252 | 91.2111 | 375 | 11 | 375 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 97.6407 | 97.4638 | 97.8182 | 91.2809 | 269 | 7 | 269 | 6 | 4 | 66.6667 | |