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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
69501-69550 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | SNP | ti | map_l150_m1_e0 | homalt | 99.7816 | 99.7680 | 99.7952 | 70.9268 | 7310 | 17 | 7310 | 15 | 6 | 40.0000 | |
| asubramanian-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.8361 | 99.8770 | 99.7952 | 51.6436 | 2436 | 3 | 2437 | 5 | 0 | 0.0000 | |
| bgallagher-sentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.8976 | 100.0000 | 99.7954 | 50.4360 | 2439 | 0 | 2439 | 5 | 0 | 0.0000 | |
| jli-custom | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.8465 | 99.8976 | 99.7954 | 28.9038 | 3902 | 4 | 3903 | 8 | 1 | 12.5000 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.8976 | 100.0000 | 99.7954 | 52.3680 | 2439 | 0 | 2439 | 5 | 0 | 0.0000 | |
| hfeng-pmm1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.3551 | 98.9186 | 99.7954 | 49.2385 | 2927 | 32 | 2927 | 6 | 0 | 0.0000 | |
| jlack-gatk | SNP | ti | map_l125_m0_e0 | homalt | 98.7968 | 97.8179 | 99.7955 | 67.3853 | 4393 | 98 | 4393 | 9 | 7 | 77.7778 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.7441 | 99.6928 | 99.7955 | 25.9231 | 3894 | 12 | 3904 | 8 | 1 | 12.5000 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.8037 | 88.4906 | 99.7955 | 45.1178 | 469 | 61 | 488 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.8037 | 88.4906 | 99.7955 | 45.1178 | 469 | 61 | 488 | 1 | 1 | 100.0000 | |
| ckim-dragen | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.8338 | 99.8720 | 99.7956 | 30.8168 | 3901 | 5 | 3905 | 8 | 4 | 50.0000 | |
| egarrison-hhga | SNP | * | map_l250_m1_e0 | homalt | 99.4705 | 99.1474 | 99.7957 | 86.3912 | 2442 | 21 | 2442 | 5 | 5 | 100.0000 | |
| egarrison-hhga | SNP | ti | map_l150_m2_e1 | * | 99.3895 | 98.9866 | 99.7957 | 75.2728 | 20513 | 210 | 20513 | 42 | 20 | 47.6190 | |
| ltrigg-rtg1 | SNP | ti | map_l125_m2_e0 | * | 99.1183 | 98.4500 | 99.7957 | 64.8854 | 29789 | 469 | 29791 | 61 | 19 | 31.1475 | |
| hfeng-pmm3 | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.2585 | 96.7678 | 99.7959 | 68.4820 | 1467 | 49 | 1467 | 3 | 1 | 33.3333 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.9097 | 88.6792 | 99.7959 | 48.3122 | 470 | 60 | 489 | 1 | 1 | 100.0000 | |
| ckim-gatk | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.7892 | 99.7825 | 99.7959 | 36.4791 | 7339 | 16 | 7335 | 15 | 5 | 33.3333 | |
| ndellapenna-hhga | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5204 | 99.2464 | 99.7960 | 35.7063 | 3424 | 26 | 3425 | 7 | 4 | 57.1429 | |
| asubramanian-gatk | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.2697 | 98.7490 | 99.7960 | 33.5412 | 2447 | 31 | 2446 | 5 | 0 | 0.0000 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 97.3586 | 95.0374 | 99.7961 | 32.0399 | 2413 | 126 | 2447 | 5 | 5 | 100.0000 | |
| dgrover-gatk | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.8437 | 99.8912 | 99.7961 | 33.9853 | 7347 | 8 | 7343 | 15 | 3 | 20.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.0156 | 88.8679 | 99.7963 | 48.3158 | 471 | 59 | 490 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 99.0215 | 98.2585 | 99.7963 | 32.1198 | 1467 | 26 | 1470 | 3 | 3 | 100.0000 | |
| ltrigg-rtg1 | SNP | * | map_l250_m1_e0 | homalt | 99.6340 | 99.4722 | 99.7963 | 86.3079 | 2450 | 13 | 2450 | 5 | 5 | 100.0000 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5935 | 99.3915 | 99.7963 | 54.1550 | 490 | 3 | 490 | 1 | 0 | 0.0000 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5935 | 99.3915 | 99.7963 | 55.2823 | 490 | 3 | 490 | 1 | 0 | 0.0000 | |
| ltrigg-rtg2 | SNP | tv | map_l125_m2_e0 | * | 98.9542 | 98.1260 | 99.7965 | 61.0321 | 16180 | 309 | 16180 | 33 | 5 | 15.1515 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6954 | 99.5943 | 99.7967 | 57.2917 | 491 | 2 | 491 | 1 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6954 | 99.5943 | 99.7967 | 57.4026 | 491 | 2 | 491 | 1 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6954 | 99.5943 | 99.7967 | 58.4810 | 491 | 2 | 491 | 1 | 0 | 0.0000 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 99.0896 | 98.3925 | 99.7967 | 32.3556 | 1469 | 24 | 1473 | 3 | 3 | 100.0000 | |
| hfeng-pmm1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 94.0613 | 88.9493 | 99.7967 | 86.1115 | 982 | 122 | 982 | 2 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6954 | 99.5943 | 99.7967 | 54.9038 | 491 | 2 | 491 | 1 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6954 | 99.5943 | 99.7967 | 58.4810 | 491 | 2 | 491 | 1 | 0 | 0.0000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 99.1576 | 98.5265 | 99.7969 | 32.7413 | 1471 | 22 | 1474 | 3 | 3 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 99.1916 | 98.5934 | 99.7970 | 32.9401 | 1472 | 21 | 1475 | 3 | 3 | 100.0000 | |
| ckim-gatk | SNP | * | HG002compoundhet | * | 99.3973 | 99.0009 | 99.7970 | 41.7198 | 25564 | 258 | 25561 | 52 | 38 | 73.0769 | |
| cchapple-custom | SNP | ti | func_cds | * | 99.8586 | 99.9202 | 99.7971 | 24.6780 | 13776 | 11 | 13774 | 28 | 1 | 3.5714 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.1781 | 98.5667 | 99.7971 | 74.2130 | 2957 | 43 | 2951 | 6 | 3 | 50.0000 | |
| rpoplin-dv42 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.7634 | 99.7296 | 99.7971 | 53.8905 | 2951 | 8 | 2951 | 6 | 1 | 16.6667 | |
| egarrison-hhga | SNP | * | map_l100_m0_e0 | * | 99.3454 | 98.8977 | 99.7972 | 67.0353 | 32479 | 362 | 32480 | 66 | 33 | 50.0000 | |
| egarrison-hhga | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.5956 | 99.3947 | 99.7973 | 28.9459 | 2463 | 15 | 2462 | 5 | 1 | 20.0000 | |
| qzeng-custom | SNP | * | HG002complexvar | het | 99.0563 | 98.3261 | 99.7975 | 19.7489 | 457708 | 7792 | 449025 | 911 | 250 | 27.4424 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 96.7615 | 93.9048 | 99.7976 | 61.1635 | 493 | 32 | 493 | 1 | 0 | 0.0000 | |
| jli-custom | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.5415 | 89.8113 | 99.7976 | 44.9275 | 476 | 54 | 493 | 1 | 1 | 100.0000 | |
| hfeng-pmm2 | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.8035 | 95.8873 | 99.7978 | 64.0929 | 2961 | 127 | 2961 | 6 | 4 | 66.6667 | |
| ltrigg-rtg1 | SNP | ti | map_l125_m2_e1 | * | 99.1256 | 98.4625 | 99.7978 | 64.9540 | 30099 | 470 | 30102 | 61 | 19 | 31.1475 | |
| astatham-gatk | SNP | tv | segdup | * | 99.1149 | 98.4412 | 99.7979 | 91.5044 | 8399 | 133 | 8395 | 17 | 6 | 35.2941 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.1986 | 94.7313 | 99.7979 | 56.1836 | 5430 | 302 | 5431 | 11 | 9 | 81.8182 | |
| astatham-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.6028 | 97.4359 | 99.7980 | 86.4421 | 494 | 13 | 494 | 1 | 1 | 100.0000 | |