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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
14151-14200 / 86044 show all | |||||||||||||||
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.5105 | 95.6899 | 99.4017 | 30.5702 | 3641 | 164 | 3655 | 22 | 22 | 100.0000 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 94.8534 | 92.9705 | 96.8142 | 85.5904 | 1640 | 124 | 1641 | 54 | 22 | 40.7407 | |
| egarrison-hhga | SNP | * | map_l150_m1_e0 | het | 99.0911 | 98.4883 | 99.7013 | 74.4872 | 19024 | 292 | 19024 | 57 | 22 | 38.5965 | |
| egarrison-hhga | SNP | * | map_l150_m2_e0 | het | 99.1156 | 98.5298 | 99.7085 | 75.6800 | 19837 | 296 | 19837 | 58 | 22 | 37.9310 | |
| egarrison-hhga | SNP | * | map_l150_m2_e1 | het | 99.1207 | 98.5415 | 99.7068 | 75.7393 | 20066 | 297 | 20066 | 59 | 22 | 37.2881 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 24.4444 | 96.6518 | 0 | 0 | 11 | 34 | 22 | 64.7059 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 0.0000 | 0.0000 | 39.3443 | 96.5321 | 0 | 0 | 24 | 37 | 22 | 59.4595 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 83.2219 | 72.1186 | 98.3665 | 35.2346 | 1314 | 508 | 1385 | 23 | 22 | 95.6522 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 93.4806 | 90.2724 | 96.9252 | 69.0862 | 1392 | 150 | 1387 | 44 | 22 | 50.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 94.5133 | 90.0694 | 99.4185 | 29.9723 | 4281 | 472 | 4274 | 25 | 22 | 88.0000 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 92.7431 | 89.6335 | 96.0762 | 74.1823 | 856 | 99 | 857 | 35 | 22 | 62.8571 | |
| 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 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.3574 | 99.5074 | 95.2984 | 84.1819 | 606 | 3 | 527 | 26 | 22 | 84.6154 | |
| ckim-vqsr | INDEL | D6_15 | HG002complexvar | het | 98.8682 | 98.6538 | 99.0835 | 59.5418 | 3078 | 42 | 3027 | 28 | 22 | 78.5714 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.8202 | 96.1199 | 99.5818 | 26.2339 | 5227 | 211 | 5239 | 22 | 22 | 100.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 83.1362 | 81.1475 | 85.2248 | 77.0629 | 396 | 92 | 398 | 69 | 22 | 31.8841 | |
| ckim-isaac | SNP | * | map_l100_m1_e0 | * | 78.4897 | 64.6727 | 99.8146 | 63.0504 | 46825 | 25578 | 46832 | 87 | 22 | 25.2874 | |
| ckim-isaac | SNP | * | map_l100_m2_e0 | * | 78.8251 | 65.1290 | 99.8156 | 65.2970 | 48172 | 25792 | 48179 | 89 | 22 | 24.7191 | |
| ckim-isaac | SNP | * | map_l100_m2_e1 | * | 78.8815 | 65.2060 | 99.8157 | 65.2814 | 48733 | 26004 | 48740 | 90 | 22 | 24.4444 | |
| ckim-vqsr | INDEL | D16_PLUS | * | homalt | 99.0314 | 99.7045 | 98.3673 | 70.9863 | 1687 | 5 | 1687 | 28 | 22 | 78.5714 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.4993 | 99.5404 | 97.4797 | 67.4289 | 1083 | 5 | 1083 | 28 | 22 | 78.5714 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.9829 | 96.4509 | 99.5644 | 27.1624 | 5245 | 193 | 5257 | 23 | 22 | 95.6522 | |
| dgrover-gatk | SNP | tv | map_l125_m1_e0 | het | 99.0398 | 99.3285 | 98.7528 | 76.5217 | 10058 | 68 | 10056 | 127 | 22 | 17.3228 | |
| dgrover-gatk | SNP | tv | map_l125_m2_e0 | het | 99.0688 | 99.3488 | 98.7904 | 77.6779 | 10374 | 68 | 10372 | 127 | 22 | 17.3228 | |
| dgrover-gatk | SNP | tv | map_l125_m2_e1 | het | 99.0786 | 99.3556 | 98.8030 | 77.7194 | 10485 | 68 | 10483 | 127 | 22 | 17.3228 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 94.4183 | 93.3511 | 95.5102 | 59.6597 | 702 | 50 | 702 | 33 | 22 | 66.6667 | |
| egarrison-hhga | INDEL | D1_5 | map_siren | * | 98.6263 | 98.6682 | 98.5844 | 80.4104 | 3482 | 47 | 3482 | 50 | 22 | 44.0000 | |
| egarrison-hhga | INDEL | D1_5 | segdup | * | 97.7335 | 97.7335 | 97.7335 | 94.3200 | 1078 | 25 | 1078 | 25 | 22 | 88.0000 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 61.8938 | 45.0533 | 98.8388 | 35.9607 | 2450 | 2988 | 2128 | 25 | 22 | 88.0000 | |
| egarrison-hhga | INDEL | D1_5 | segdup | het | 98.1532 | 99.7110 | 96.6434 | 93.9982 | 690 | 2 | 691 | 24 | 21 | 87.5000 | |
| egarrison-hhga | INDEL | D6_15 | map_siren | * | 91.4556 | 90.1768 | 92.7711 | 83.2942 | 459 | 50 | 462 | 36 | 21 | 58.3333 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.7250 | 99.6324 | 97.8339 | 67.7720 | 1084 | 4 | 1084 | 24 | 21 | 87.5000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 83.4086 | 85.9259 | 81.0345 | 77.7778 | 116 | 19 | 94 | 22 | 21 | 95.4545 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.5308 | 95.5496 | 99.5959 | 50.2969 | 5668 | 264 | 5668 | 23 | 21 | 91.3043 | |
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4006 | 99.5116 | 99.2899 | 63.6333 | 35246 | 173 | 35235 | 252 | 21 | 8.3333 | |
| egarrison-hhga | INDEL | I6_15 | HG002complexvar | hetalt | 95.1315 | 92.3957 | 98.0342 | 53.6450 | 1130 | 93 | 1147 | 23 | 21 | 91.3043 | |
| egarrison-hhga | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.5362 | 98.1948 | 98.8800 | 67.3655 | 4678 | 86 | 4679 | 53 | 21 | 39.6226 | |
| egarrison-hhga | SNP | ti | HG002compoundhet | het | 98.7211 | 97.8643 | 99.5931 | 37.6968 | 9302 | 203 | 9300 | 38 | 21 | 55.2632 | |
| egarrison-hhga | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4577 | 99.1576 | 99.7596 | 63.2532 | 17420 | 148 | 17430 | 42 | 21 | 50.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.2135 | 97.8118 | 98.6185 | 35.4245 | 2235 | 50 | 2213 | 31 | 21 | 67.7419 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 92.2495 | 86.6245 | 98.6558 | 36.0651 | 2053 | 317 | 2055 | 28 | 21 | 75.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 84.1772 | 73.3974 | 98.6684 | 34.6801 | 2290 | 830 | 2297 | 31 | 21 | 67.7419 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5326 | 98.2332 | 92.9766 | 69.7368 | 278 | 5 | 278 | 21 | 21 | 100.0000 | |
| dgrover-gatk | SNP | ti | HG002compoundhet | * | 99.8369 | 99.8284 | 99.8455 | 35.6925 | 17448 | 30 | 17446 | 27 | 21 | 77.7778 | |
| dgrover-gatk | SNP | tv | HG002complexvar | het | 99.9396 | 99.9138 | 99.9655 | 21.5720 | 150601 | 130 | 150525 | 52 | 21 | 40.3846 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.5363 | 99.2878 | 99.7860 | 56.6980 | 16312 | 117 | 16318 | 35 | 21 | 60.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 97.0472 | 97.6240 | 96.4773 | 83.0378 | 945 | 23 | 849 | 31 | 21 | 67.7419 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 96.7853 | 97.1074 | 96.4652 | 83.3460 | 940 | 28 | 846 | 31 | 21 | 67.7419 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 83.0580 | 85.1852 | 81.0345 | 77.8626 | 115 | 20 | 94 | 22 | 21 | 95.4545 | |