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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
49751-49800 / 86044 show all | |||||||||||||||
| anovak-vg | SNP | tv | tech_badpromoters | homalt | 93.1507 | 87.1795 | 100.0000 | 36.5385 | 34 | 5 | 33 | 0 | 0 | ||
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.7788 | 99.3179 | 98.2456 | 73.2684 | 728 | 5 | 728 | 13 | 13 | 100.0000 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 85.5072 | 98.6072 | 75.4797 | 48.5181 | 354 | 5 | 354 | 115 | 114 | 99.1304 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.6744 | 99.4583 | 99.8915 | 29.8859 | 918 | 5 | 921 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | D16_PLUS | * | homalt | 99.1187 | 99.7045 | 98.5397 | 70.8497 | 1687 | 5 | 1687 | 25 | 20 | 80.0000 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.8086 | 99.5997 | 98.0299 | 75.0492 | 1244 | 5 | 1244 | 25 | 20 | 80.0000 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.0036 | 97.5124 | 96.5000 | 88.7577 | 196 | 5 | 193 | 7 | 1 | 14.2857 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5140 | 99.3932 | 99.6350 | 71.2386 | 819 | 5 | 819 | 3 | 1 | 33.3333 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.8086 | 99.5997 | 98.0299 | 75.0492 | 1244 | 5 | 1244 | 25 | 20 | 80.0000 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.1121 | 98.7531 | 99.4737 | 81.8095 | 396 | 5 | 378 | 2 | 1 | 50.0000 | |
| astatham-gatk | INDEL | D16_PLUS | map_l100_m2_e1 | hetalt | 90.9091 | 83.3333 | 100.0000 | 78.2258 | 25 | 5 | 27 | 0 | 0 | ||
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5144 | 99.6757 | 99.3536 | 78.0162 | 1537 | 5 | 1537 | 10 | 5 | 50.0000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.0508 | 99.8948 | 98.2209 | 50.1958 | 4748 | 5 | 4748 | 86 | 85 | 98.8372 | |
| astatham-gatk | INDEL | D1_5 | map_siren | hetalt | 96.9325 | 94.0476 | 100.0000 | 90.6176 | 79 | 5 | 79 | 0 | 0 | ||
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 97.2266 | 98.4848 | 96.0000 | 75.7282 | 325 | 5 | 312 | 13 | 7 | 53.8462 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.6431 | 99.2888 | 100.0000 | 46.4313 | 698 | 5 | 698 | 0 | 0 | ||
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 97.5038 | 96.4789 | 98.5507 | 46.5116 | 137 | 5 | 136 | 2 | 1 | 50.0000 | |
| astatham-gatk | INDEL | D6_15 | map_l100_m1_e0 | hetalt | 96.1832 | 92.6471 | 100.0000 | 72.7273 | 63 | 5 | 63 | 0 | 0 | ||
| astatham-gatk | INDEL | D6_15 | map_l100_m2_e0 | hetalt | 96.1832 | 92.6471 | 100.0000 | 74.2857 | 63 | 5 | 63 | 0 | 0 | ||
| astatham-gatk | INDEL | D6_15 | map_l125_m2_e0 | * | 97.1888 | 96.0317 | 98.3740 | 91.4226 | 121 | 5 | 121 | 2 | 1 | 50.0000 | |
| astatham-gatk | INDEL | D6_15 | map_siren | hetalt | 97.4093 | 94.9495 | 100.0000 | 75.7106 | 94 | 5 | 94 | 0 | 0 | ||
| astatham-gatk | INDEL | D6_15 | segdup | hetalt | 94.6237 | 89.7959 | 100.0000 | 90.3720 | 44 | 5 | 44 | 0 | 0 | ||
| astatham-gatk | INDEL | I16_PLUS | * | homalt | 97.6467 | 99.6797 | 95.6950 | 72.0858 | 1556 | 5 | 1556 | 70 | 68 | 97.1429 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.5959 | 94.7368 | 96.4706 | 90.8504 | 90 | 5 | 82 | 3 | 0 | 0.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5326 | 98.2332 | 92.9766 | 69.5519 | 278 | 5 | 278 | 21 | 21 | 100.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4789 | 99.8586 | 99.1021 | 72.7252 | 3532 | 5 | 3532 | 32 | 32 | 100.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 93.5774 | 90.1961 | 97.2222 | 94.2308 | 46 | 5 | 35 | 1 | 0 | 0.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.6188 | 99.5238 | 99.7140 | 62.1846 | 1045 | 5 | 1046 | 3 | 3 | 100.0000 | |
| astatham-gatk | INDEL | I1_5 | map_l250_m1_e0 | * | 95.7346 | 95.2830 | 96.1905 | 96.1024 | 101 | 5 | 101 | 4 | 2 | 50.0000 | |
| astatham-gatk | INDEL | I1_5 | map_l250_m1_e0 | het | 94.0171 | 91.6667 | 96.4912 | 96.8733 | 55 | 5 | 55 | 2 | 0 | 0.0000 | |
| astatham-gatk | INDEL | I6_15 | HG002compoundhet | het | 85.7861 | 97.5962 | 76.5258 | 84.3382 | 203 | 5 | 163 | 50 | 49 | 98.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3499 | 98.9224 | 99.7812 | 72.1171 | 459 | 5 | 456 | 1 | 0 | 0.0000 | |
| astatham-gatk | INDEL | I6_15 | map_l125_m1_e0 | * | 93.2039 | 90.5660 | 96.0000 | 91.9094 | 48 | 5 | 48 | 2 | 1 | 50.0000 | |
| astatham-gatk | INDEL | I6_15 | map_l125_m2_e0 | * | 93.2039 | 90.5660 | 96.0000 | 92.7641 | 48 | 5 | 48 | 2 | 1 | 50.0000 | |
| astatham-gatk | INDEL | I6_15 | map_l125_m2_e1 | * | 93.2039 | 90.5660 | 96.0000 | 92.9478 | 48 | 5 | 48 | 2 | 1 | 50.0000 | |
| astatham-gatk | SNP | * | func_cds | homalt | 99.9642 | 99.9284 | 100.0000 | 20.9745 | 6974 | 5 | 6974 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.4449 | 99.3179 | 97.5871 | 73.2136 | 728 | 5 | 728 | 18 | 14 | 77.7778 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 97.6981 | 96.2121 | 99.2308 | 79.2000 | 127 | 5 | 129 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.2777 | 97.5124 | 95.0739 | 88.5181 | 196 | 5 | 193 | 10 | 1 | 10.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3205 | 99.5404 | 97.1300 | 67.2155 | 1083 | 5 | 1083 | 32 | 26 | 81.2500 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 92.1348 | 89.1304 | 95.3488 | 68.6131 | 41 | 5 | 41 | 2 | 2 | 100.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | map_l100_m2_e1 | hetalt | 90.9091 | 83.3333 | 100.0000 | 78.4000 | 25 | 5 | 27 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.1735 | 98.8506 | 97.5057 | 69.0309 | 430 | 5 | 430 | 11 | 5 | 45.4545 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5466 | 99.6757 | 99.4179 | 77.8922 | 1537 | 5 | 1537 | 9 | 5 | 55.5556 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.8468 | 99.7812 | 99.9125 | 46.5872 | 2280 | 5 | 2283 | 2 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l125_m0_e0 | * | 97.9095 | 98.9919 | 96.8504 | 88.8865 | 491 | 5 | 492 | 16 | 3 | 18.7500 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l150_m2_e1 | het | 97.8305 | 99.0421 | 96.6480 | 89.9495 | 517 | 5 | 519 | 18 | 3 | 16.6667 | |
| bgallagher-sentieon | INDEL | D1_5 | map_siren | hetalt | 96.3415 | 94.0476 | 98.7500 | 89.6507 | 79 | 5 | 79 | 1 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5522 | 99.5025 | 99.6020 | 65.6057 | 1000 | 5 | 1001 | 4 | 3 | 75.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 93.6937 | 91.2281 | 96.2963 | 99.4858 | 52 | 5 | 52 | 2 | 0 | 0.0000 | |