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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16001-16050 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.3536 | 99.6296 | 99.0792 | 82.1733 | 538 | 2 | 538 | 5 | 4 | 80.0000 | |
| jmaeng-gatk | INDEL | I1_5 | map_siren | homalt | 99.5051 | 99.4224 | 99.5878 | 78.4891 | 1205 | 7 | 1208 | 5 | 4 | 80.0000 | |
| jpowers-varprowl | INDEL | * | map_l100_m2_e1 | * | 91.1487 | 89.5367 | 92.8197 | 85.5685 | 3363 | 393 | 3361 | 260 | 208 | 80.0000 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.3346 | 95.0228 | 99.7616 | 43.5987 | 2081 | 109 | 2092 | 5 | 4 | 80.0000 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.5615 | 99.2123 | 99.9132 | 66.4238 | 11461 | 91 | 11511 | 10 | 8 | 80.0000 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.5615 | 99.2123 | 99.9132 | 66.4238 | 11461 | 91 | 11511 | 10 | 8 | 80.0000 | |
| jmaeng-gatk | INDEL | * | map_l150_m2_e1 | homalt | 98.5714 | 98.1707 | 98.9754 | 89.5771 | 483 | 9 | 483 | 5 | 4 | 80.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.8483 | 99.0025 | 98.6945 | 81.4707 | 397 | 4 | 378 | 5 | 4 | 80.0000 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.3525 | 99.2040 | 99.5015 | 66.2630 | 997 | 8 | 998 | 5 | 4 | 80.0000 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.4204 | 99.1329 | 99.7095 | 36.8209 | 1715 | 15 | 1716 | 5 | 4 | 80.0000 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 94.9225 | 92.5121 | 97.4619 | 73.8553 | 383 | 31 | 384 | 10 | 8 | 80.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.2315 | 88.9794 | 97.9104 | 67.2852 | 1639 | 203 | 1640 | 35 | 28 | 80.0000 | |
| 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 | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.5608 | 96.7376 | 96.3847 | 75.3388 | 1364 | 46 | 1333 | 50 | 40 | 80.0000 | |
| 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 | |
| ckim-isaac | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 97.8767 | 95.9619 | 99.8695 | 26.2226 | 3826 | 161 | 3827 | 5 | 4 | 80.0000 | |
| ckim-isaac | SNP | tv | HG002complexvar | homalt | 95.1060 | 90.6877 | 99.9768 | 19.5838 | 86254 | 8857 | 86277 | 20 | 16 | 80.0000 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 95.7008 | 92.5507 | 99.0729 | 30.3936 | 3193 | 257 | 3206 | 30 | 24 | 80.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002complexvar | homalt | 98.7952 | 99.3080 | 98.2877 | 76.3371 | 287 | 2 | 287 | 5 | 4 | 80.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 95.1278 | 98.7805 | 91.7355 | 88.1139 | 162 | 2 | 111 | 10 | 8 | 80.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.5967 | 99.5697 | 99.6236 | 75.3470 | 33093 | 143 | 33087 | 125 | 100 | 80.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 82.2581 | 75.0000 | 91.0714 | 96.6981 | 51 | 17 | 51 | 5 | 4 | 80.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l100_m1_e0 | homalt | 99.2405 | 99.3243 | 99.1568 | 82.6608 | 588 | 4 | 588 | 5 | 4 | 80.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l100_m2_e0 | homalt | 99.2641 | 99.3453 | 99.1830 | 83.4862 | 607 | 4 | 607 | 5 | 4 | 80.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l100_m2_e1 | homalt | 99.1935 | 99.1935 | 99.1935 | 83.6066 | 615 | 5 | 615 | 5 | 4 | 80.0000 | |
| egarrison-hhga | INDEL | D6_15 | map_l125_m1_e0 | het | 94.9763 | 96.8750 | 93.1507 | 89.2647 | 62 | 2 | 68 | 5 | 4 | 80.0000 | |
| egarrison-hhga | INDEL | D6_15 | map_l125_m2_e0 | het | 95.4357 | 97.1831 | 93.7500 | 89.2905 | 69 | 2 | 75 | 5 | 4 | 80.0000 | |
| egarrison-hhga | INDEL | D6_15 | map_l125_m2_e1 | het | 95.4357 | 97.1831 | 93.7500 | 89.5288 | 69 | 2 | 75 | 5 | 4 | 80.0000 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 97.7556 | 98.0000 | 97.5124 | 66.4441 | 196 | 4 | 196 | 5 | 4 | 80.0000 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 88.2868 | 81.1828 | 96.7532 | 67.3729 | 151 | 35 | 149 | 5 | 4 | 80.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 82.4914 | 70.8428 | 98.7245 | 40.6959 | 311 | 128 | 387 | 5 | 4 | 80.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 81.4240 | 70.4268 | 96.4912 | 53.1250 | 231 | 97 | 275 | 10 | 8 | 80.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 83.9902 | 73.3509 | 98.2394 | 46.3138 | 278 | 101 | 279 | 5 | 4 | 80.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 78.7936 | 69.0909 | 91.6667 | 70.8738 | 38 | 17 | 55 | 5 | 4 | 80.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 94.7121 | 90.9707 | 98.7745 | 28.0423 | 403 | 40 | 403 | 5 | 4 | 80.0000 | |
| ckim-isaac | INDEL | D6_15 | map_l100_m1_e0 | * | 65.8098 | 50.0000 | 96.2406 | 83.4577 | 129 | 129 | 128 | 5 | 4 | 80.0000 | |
| ckim-isaac | INDEL | D6_15 | map_l100_m2_e0 | * | 65.8291 | 50.0000 | 96.3235 | 84.3858 | 132 | 132 | 131 | 5 | 4 | 80.0000 | |
| ckim-isaac | INDEL | D6_15 | map_l100_m2_e1 | * | 65.3788 | 49.4545 | 96.4286 | 84.2697 | 136 | 139 | 135 | 5 | 4 | 80.0000 | |
| ckim-isaac | INDEL | D6_15 | map_siren | het | 69.0327 | 54.6429 | 93.7107 | 81.3380 | 153 | 127 | 149 | 10 | 8 | 80.0000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 73.7864 | 82.6087 | 66.6667 | 70.8738 | 19 | 4 | 20 | 10 | 8 | 80.0000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 72.0000 | 81.8182 | 64.2857 | 67.4419 | 18 | 4 | 18 | 10 | 8 | 80.0000 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 94.8810 | 91.7722 | 98.2079 | 71.1479 | 290 | 26 | 274 | 5 | 4 | 80.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_siren | homalt | 99.4864 | 99.4007 | 99.5723 | 81.4444 | 1161 | 7 | 1164 | 5 | 4 | 80.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.2927 | 98.9965 | 99.5907 | 51.8966 | 3650 | 37 | 3650 | 15 | 12 | 80.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.7147 | 100.0000 | 97.4619 | 47.3262 | 192 | 0 | 192 | 5 | 4 | 80.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 94.0845 | 91.8750 | 96.4029 | 90.0144 | 147 | 13 | 134 | 5 | 4 | 80.0000 | |
| ckim-vqsr | INDEL | I6_15 | HG002complexvar | het | 99.2942 | 98.8110 | 99.7821 | 59.6661 | 2327 | 28 | 2290 | 5 | 4 | 80.0000 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.5470 | 99.1558 | 99.9413 | 57.3410 | 17032 | 145 | 17028 | 10 | 8 | 80.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.5016 | 99.4565 | 99.5467 | 86.5782 | 1098 | 6 | 1098 | 5 | 4 | 80.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.4452 | 99.5833 | 99.3075 | 87.8041 | 717 | 3 | 717 | 5 | 4 | 80.0000 | |