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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
18801-18850 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | I16_PLUS | * | het | 98.1949 | 97.2774 | 99.1298 | 76.5400 | 2644 | 74 | 2620 | 23 | 10 | 43.4783 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.6522 | 99.1803 | 92.3664 | 87.2444 | 121 | 1 | 121 | 10 | 10 | 100.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 94.6645 | 92.0290 | 97.4555 | 73.3740 | 381 | 33 | 383 | 10 | 10 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.2085 | 91.0448 | 97.6000 | 62.4906 | 488 | 48 | 488 | 12 | 10 | 83.3333 | |
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.1361 | 98.7615 | 99.5135 | 67.2304 | 4705 | 59 | 4705 | 23 | 10 | 43.4783 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.4293 | 99.3243 | 99.5345 | 87.4555 | 2352 | 16 | 2352 | 11 | 10 | 90.9091 | |
| ckim-vqsr | SNP | ti | map_l100_m1_e0 | het | 85.6453 | 75.3523 | 99.1953 | 82.9534 | 22562 | 7380 | 22557 | 183 | 10 | 5.4645 | |
| ckim-vqsr | INDEL | I16_PLUS | HG002complexvar | * | 98.2632 | 97.2498 | 99.2980 | 66.9502 | 1273 | 36 | 1273 | 9 | 9 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.3268 | 94.9581 | 99.8166 | 57.9977 | 5443 | 289 | 5444 | 10 | 9 | 90.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 92.9134 | 100.0000 | 86.7647 | 76.7123 | 59 | 0 | 59 | 9 | 9 | 100.0000 | |
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.9186 | 98.5743 | 99.2654 | 69.9659 | 2973 | 43 | 2973 | 22 | 9 | 40.9091 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.3727 | 99.4055 | 99.3399 | 88.6347 | 1505 | 9 | 1505 | 10 | 9 | 90.0000 | |
| ckim-vqsr | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.5289 | 99.3598 | 99.6985 | 56.1737 | 27780 | 179 | 27779 | 84 | 9 | 10.7143 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.5262 | 99.3991 | 99.6536 | 77.7226 | 6617 | 40 | 6617 | 23 | 9 | 39.1304 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 83.1458 | 71.4848 | 99.3528 | 29.1555 | 1815 | 724 | 1842 | 12 | 9 | 75.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 85.1654 | 74.5662 | 99.2771 | 27.6058 | 1633 | 557 | 1648 | 12 | 9 | 75.0000 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.5449 | 91.7497 | 99.6677 | 68.0131 | 3592 | 323 | 3599 | 12 | 9 | 75.0000 | |
| ckim-isaac | SNP | * | map_l100_m0_e0 | * | 74.0949 | 58.9233 | 99.7886 | 67.9602 | 19351 | 13490 | 19354 | 41 | 9 | 21.9512 | |
| ckim-isaac | SNP | * | map_l150_m2_e1 | het | 74.2817 | 59.2251 | 99.6036 | 80.2344 | 12060 | 8303 | 12061 | 48 | 9 | 18.7500 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 91.8799 | 87.4858 | 96.7387 | 79.1713 | 2314 | 331 | 2373 | 80 | 9 | 11.2500 | |
| ckim-isaac | SNP | tv | map_l125_m1_e0 | * | 70.3696 | 54.3831 | 99.6682 | 71.7978 | 8710 | 7306 | 8712 | 29 | 9 | 31.0345 | |
| ckim-isaac | SNP | tv | map_l125_m2_e0 | * | 70.8343 | 54.9397 | 99.6700 | 73.8494 | 9059 | 7430 | 9061 | 30 | 9 | 30.0000 | |
| ckim-isaac | SNP | tv | map_l125_m2_e1 | * | 70.9236 | 55.0459 | 99.6739 | 73.8556 | 9169 | 7488 | 9171 | 30 | 9 | 30.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.6908 | 99.5935 | 97.8044 | 62.6398 | 490 | 2 | 490 | 11 | 9 | 81.8182 | |
| ckim-vqsr | INDEL | * | segdup | homalt | 99.3776 | 99.7917 | 98.9669 | 93.6950 | 958 | 2 | 958 | 10 | 9 | 90.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 95.2725 | 91.6923 | 99.1437 | 39.7362 | 894 | 81 | 1042 | 9 | 9 | 100.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 96.9627 | 94.4899 | 99.5685 | 38.0503 | 3464 | 202 | 3461 | 15 | 9 | 60.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 92.4298 | 90.2778 | 94.6869 | 59.3991 | 520 | 56 | 499 | 28 | 9 | 32.1429 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 85.6061 | 79.5775 | 92.6230 | 28.6550 | 113 | 29 | 113 | 9 | 9 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | het | 71.6186 | 79.1667 | 65.3846 | 43.4783 | 19 | 5 | 17 | 9 | 9 | 100.0000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 68.5714 | 57.1429 | 85.7143 | 76.6667 | 76 | 57 | 78 | 13 | 9 | 69.2308 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 70.9431 | 59.3496 | 88.1657 | 78.6885 | 146 | 100 | 149 | 20 | 9 | 45.0000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 77.6371 | 75.4098 | 80.0000 | 77.2727 | 46 | 15 | 48 | 12 | 9 | 75.0000 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 96.1245 | 94.5714 | 97.7295 | 52.4859 | 993 | 57 | 990 | 23 | 9 | 39.1304 | |
| dgrover-gatk | INDEL | I16_PLUS | * | het | 98.6296 | 98.3076 | 98.9537 | 76.0151 | 2672 | 46 | 2648 | 28 | 9 | 32.1429 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.4319 | 93.2367 | 97.7330 | 74.4530 | 386 | 28 | 388 | 9 | 9 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | HG002complexvar | het | 99.7798 | 99.6646 | 99.8952 | 58.2404 | 18128 | 61 | 18108 | 19 | 9 | 47.3684 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.3090 | 96.8597 | 99.8023 | 58.5209 | 5552 | 180 | 5553 | 11 | 9 | 81.8182 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.7064 | 91.7910 | 97.8131 | 63.8129 | 492 | 44 | 492 | 11 | 9 | 81.8182 | |
| dgrover-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.2427 | 99.0344 | 99.4519 | 67.0189 | 4718 | 46 | 4718 | 26 | 9 | 34.6154 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.5351 | 99.4510 | 99.6193 | 87.6224 | 2355 | 13 | 2355 | 9 | 9 | 100.0000 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.5051 | 99.6037 | 99.4067 | 88.7962 | 1508 | 6 | 1508 | 9 | 9 | 100.0000 | |
| dgrover-gatk | SNP | * | map_l100_m0_e0 | homalt | 99.5293 | 99.1738 | 99.8873 | 60.6890 | 11524 | 96 | 11524 | 13 | 9 | 69.2308 | |
| dgrover-gatk | SNP | * | segdup | homalt | 99.8976 | 99.8790 | 99.9162 | 88.2042 | 10730 | 13 | 10730 | 9 | 9 | 100.0000 | |
| dgrover-gatk | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.7116 | 99.6705 | 99.7527 | 66.8941 | 4840 | 16 | 4840 | 12 | 9 | 75.0000 | |
| dgrover-gatk | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.6764 | 99.7409 | 99.6119 | 69.3315 | 3080 | 8 | 3080 | 12 | 9 | 75.0000 | |
| dgrover-gatk | SNP | tv | map_l250_m2_e0 | het | 97.7378 | 97.9897 | 97.4872 | 91.2583 | 1901 | 39 | 1901 | 49 | 9 | 18.3673 | |
| dgrover-gatk | SNP | tv | map_l250_m2_e1 | het | 97.7665 | 98.0153 | 97.5190 | 91.3080 | 1926 | 39 | 1926 | 49 | 9 | 18.3673 | |
| dgrover-gatk | SNP | tv | map_siren | homalt | 99.7938 | 99.6520 | 99.9360 | 53.0780 | 17180 | 60 | 17177 | 11 | 9 | 81.8182 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 80.7503 | 68.3682 | 98.6094 | 40.8377 | 817 | 378 | 780 | 11 | 9 | 81.8182 | |