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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
55101-55150 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 86.4727 | 80.3922 | 93.5484 | 94.4840 | 41 | 10 | 29 | 2 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m1_e0 | * | 98.9155 | 98.7952 | 99.0361 | 84.0996 | 820 | 10 | 822 | 8 | 2 | 25.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m1_e0 | het | 98.4509 | 97.9424 | 98.9648 | 85.0418 | 476 | 10 | 478 | 5 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | map_l100_m1_e0 | * | 94.9772 | 91.2281 | 99.0476 | 85.2941 | 104 | 10 | 104 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | map_l100_m2_e0 | * | 95.0673 | 91.3793 | 99.0654 | 86.3520 | 106 | 10 | 106 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | map_l100_m2_e1 | * | 95.0673 | 91.3793 | 99.0654 | 86.7081 | 106 | 10 | 106 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | map_siren | het | 96.0289 | 93.0070 | 99.2537 | 83.7181 | 133 | 10 | 133 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 75.5556 | 62.9630 | 94.4444 | 97.9310 | 17 | 10 | 17 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | SNP | * | map_l250_m1_e0 | homalt | 99.4527 | 99.5940 | 99.3117 | 86.9423 | 2453 | 10 | 2453 | 17 | 6 | 35.2941 | |
| jlack-gatk | INDEL | * | map_l150_m0_e0 | het | 88.0882 | 97.0674 | 80.6295 | 94.9157 | 331 | 10 | 333 | 80 | 1 | 1.2500 | |
| jlack-gatk | INDEL | * | map_l250_m1_e0 | * | 89.9390 | 96.7213 | 84.0456 | 96.8466 | 295 | 10 | 295 | 56 | 4 | 7.1429 | |
| jlack-gatk | INDEL | * | map_l250_m2_e0 | * | 90.6780 | 96.9789 | 85.1459 | 97.0399 | 321 | 10 | 321 | 56 | 4 | 7.1429 | |
| jlack-gatk | INDEL | * | map_l250_m2_e1 | * | 90.7303 | 96.9970 | 85.2243 | 97.1042 | 323 | 10 | 323 | 56 | 4 | 7.1429 | |
| jlack-gatk | INDEL | D16_PLUS | HG002compoundhet | het | 80.6922 | 97.5309 | 68.8119 | 59.1507 | 395 | 10 | 278 | 126 | 121 | 96.0317 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.8912 | 97.3958 | 96.3918 | 85.9420 | 374 | 10 | 374 | 14 | 3 | 21.4286 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 61.2613 | 77.2727 | 50.7463 | 95.1868 | 34 | 10 | 34 | 33 | 3 | 9.0909 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.9263 | 97.7011 | 98.1524 | 69.9306 | 425 | 10 | 425 | 8 | 5 | 62.5000 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.3837 | 99.3515 | 99.4160 | 78.0297 | 1532 | 10 | 1532 | 9 | 5 | 55.5556 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.0972 | 99.7896 | 96.4613 | 40.7376 | 4743 | 10 | 4743 | 174 | 174 | 100.0000 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 60.3960 | 85.9155 | 46.5649 | 47.8088 | 61 | 10 | 61 | 70 | 70 | 100.0000 | |
| jlack-gatk | INDEL | D1_5 | map_l150_m1_e0 | * | 92.6175 | 98.6053 | 87.3153 | 91.1605 | 707 | 10 | 709 | 103 | 4 | 3.8835 | |
| jlack-gatk | INDEL | D1_5 | map_l150_m2_e0 | * | 92.9788 | 98.6894 | 87.8929 | 91.6415 | 753 | 10 | 755 | 104 | 4 | 3.8462 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.0270 | 99.5781 | 96.5235 | 48.1882 | 2360 | 10 | 2360 | 85 | 84 | 98.8235 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 41.2281 | 82.4561 | 27.4854 | 98.2013 | 47 | 10 | 47 | 124 | 2 | 1.6129 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.9618 | 99.7173 | 98.2178 | 72.3769 | 3527 | 10 | 3527 | 64 | 63 | 98.4375 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.6744 | 97.1098 | 98.2456 | 68.8808 | 336 | 10 | 336 | 6 | 3 | 50.0000 | |
| jlack-gatk | INDEL | I1_5 | map_l125_m1_e0 | het | 94.8373 | 97.9424 | 91.9231 | 91.0821 | 476 | 10 | 478 | 42 | 2 | 4.7619 | |
| jlack-gatk | INDEL | I1_5 | map_l125_m2_e0 | het | 94.4890 | 97.9879 | 91.2313 | 91.8168 | 487 | 10 | 489 | 47 | 3 | 6.3830 | |
| jlack-gatk | INDEL | I1_5 | map_l125_m2_e1 | het | 94.5144 | 98.0315 | 91.2409 | 91.8416 | 498 | 10 | 500 | 48 | 3 | 6.2500 | |
| jlack-gatk | INDEL | I1_5 | map_l150_m1_e0 | * | 95.4901 | 98.0237 | 93.0841 | 91.9135 | 496 | 10 | 498 | 37 | 4 | 10.8108 | |
| jlack-gatk | INDEL | I1_5 | map_l150_m2_e0 | * | 95.3323 | 98.0732 | 92.7405 | 92.6709 | 509 | 10 | 511 | 40 | 4 | 10.0000 | |
| jlack-gatk | INDEL | I1_5 | map_l150_m2_e1 | * | 95.3476 | 98.1168 | 92.7305 | 92.6905 | 521 | 10 | 523 | 41 | 4 | 9.7561 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.2339 | 98.8263 | 99.6450 | 83.3103 | 842 | 10 | 842 | 3 | 3 | 100.0000 | |
| jlack-gatk | SNP | ti | HG002compoundhet | homalt | 99.8918 | 99.8648 | 99.9188 | 30.3225 | 7384 | 10 | 7384 | 6 | 6 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 99.5082 | 99.1830 | 99.8355 | 58.4841 | 1214 | 10 | 1214 | 2 | 2 | 100.0000 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 95.9752 | 93.9394 | 98.1013 | 91.0986 | 155 | 10 | 155 | 3 | 2 | 66.6667 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.5984 | 99.3324 | 99.8658 | 78.7628 | 1488 | 10 | 1488 | 2 | 2 | 100.0000 | |
| jlack-gatk | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8006 | 99.8575 | 99.7437 | 62.4217 | 7009 | 10 | 7005 | 18 | 3 | 16.6667 | |
| jlack-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.1720 | 99.8658 | 94.6197 | 41.0468 | 7442 | 10 | 7439 | 423 | 4 | 0.9456 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.4343 | 98.6357 | 98.2337 | 71.3284 | 723 | 10 | 723 | 13 | 9 | 69.2308 | |
| jli-custom | INDEL | * | map_l100_m1_e0 | homalt | 99.1850 | 99.1850 | 99.1850 | 82.2765 | 1217 | 10 | 1217 | 10 | 6 | 60.0000 | |
| jli-custom | INDEL | * | map_l100_m2_e0 | homalt | 99.1284 | 99.2070 | 99.0499 | 83.3333 | 1251 | 10 | 1251 | 12 | 6 | 50.0000 | |
| jli-custom | INDEL | * | map_l100_m2_e1 | homalt | 99.1420 | 99.2194 | 99.0647 | 83.4066 | 1271 | 10 | 1271 | 12 | 6 | 50.0000 | |
| jli-custom | INDEL | * | map_l150_m0_e0 | het | 97.0674 | 97.0674 | 97.0674 | 91.5678 | 331 | 10 | 331 | 10 | 1 | 10.0000 | |
| hfeng-pmm2 | SNP | * | map_l250_m2_e0 | homalt | 99.4980 | 99.6277 | 99.3687 | 87.8966 | 2676 | 10 | 2676 | 17 | 6 | 35.2941 | |
| hfeng-pmm2 | SNP | * | map_l250_m2_e1 | homalt | 99.5040 | 99.6321 | 99.3761 | 87.9531 | 2708 | 10 | 2708 | 17 | 6 | 35.2941 | |
| hfeng-pmm2 | SNP | tv | map_l125_m0_e0 | homalt | 99.5050 | 99.5498 | 99.4602 | 72.5691 | 2211 | 10 | 2211 | 12 | 4 | 33.3333 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9159 | 99.9115 | 99.9203 | 55.8220 | 11286 | 10 | 11286 | 9 | 9 | 100.0000 | |
| hfeng-pmm3 | INDEL | * | segdup | hetalt | 96.0000 | 92.3077 | 100.0000 | 94.6374 | 120 | 10 | 122 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.2177 | 99.0809 | 99.3548 | 63.5417 | 1078 | 10 | 1078 | 7 | 4 | 57.1429 | |