PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
63701-63750 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 95.4677 | 94.4444 | 96.5135 | 88.1879 | 629 | 37 | 609 | 22 | 5 | 22.7273 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 94.7368 | 100.0000 | 90.0000 | 82.8179 | 45 | 0 | 45 | 5 | 5 | 100.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.3273 | 91.1635 | 99.8897 | 40.2875 | 5375 | 521 | 5435 | 6 | 5 | 83.3333 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.3273 | 91.1635 | 99.8897 | 40.2875 | 5375 | 521 | 5435 | 6 | 5 | 83.3333 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.1117 | 98.9729 | 99.2509 | 77.5593 | 1349 | 14 | 1325 | 10 | 5 | 50.0000 | |
| jlack-gatk | INDEL | I1_5 | map_l125_m2_e0 | * | 96.2945 | 98.3664 | 94.3080 | 90.1657 | 843 | 14 | 845 | 51 | 5 | 9.8039 | |
| jlack-gatk | INDEL | I1_5 | map_l125_m2_e1 | * | 96.2945 | 98.3908 | 94.2857 | 90.2392 | 856 | 14 | 858 | 52 | 5 | 9.6154 | |
| jlack-gatk | INDEL | I1_5 | map_siren | het | 96.7640 | 98.4533 | 95.1317 | 84.9119 | 1655 | 26 | 1661 | 85 | 5 | 5.8824 | |
| jlack-gatk | INDEL | I1_5 | map_siren | homalt | 99.3823 | 99.4224 | 99.3421 | 78.6217 | 1205 | 7 | 1208 | 8 | 5 | 62.5000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 97.5769 | 96.6102 | 98.5632 | 70.4835 | 342 | 12 | 343 | 5 | 5 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.2618 | 91.9463 | 94.6154 | 77.5475 | 137 | 12 | 123 | 7 | 5 | 71.4286 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.6416 | 99.4125 | 99.8717 | 75.1815 | 3892 | 23 | 3892 | 5 | 5 | 100.0000 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9343 | 99.9507 | 99.9179 | 54.3410 | 6085 | 3 | 6085 | 5 | 5 | 100.0000 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5118 | 99.8232 | 99.2024 | 37.2444 | 7342 | 13 | 7338 | 59 | 5 | 8.4746 | |
| jlack-gatk | SNP | * | segdup | het | 97.2497 | 99.7806 | 94.8441 | 94.7945 | 17279 | 38 | 17273 | 939 | 5 | 0.5325 | |
| jlack-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.7667 | 98.9130 | 98.6207 | 68.3258 | 2002 | 22 | 2002 | 28 | 5 | 17.8571 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.7223 | 99.4893 | 99.9565 | 63.3985 | 11493 | 59 | 11493 | 5 | 5 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 96.3636 | 95.9276 | 96.8037 | 90.7789 | 212 | 9 | 212 | 7 | 5 | 71.4286 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 96.7532 | 98.0263 | 95.5128 | 90.8612 | 149 | 3 | 149 | 7 | 5 | 71.4286 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.7223 | 99.4893 | 99.9565 | 63.3985 | 11493 | 59 | 11493 | 5 | 5 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0614 | 99.8136 | 98.3203 | 43.6922 | 10712 | 20 | 10712 | 183 | 5 | 2.7322 | |
| jlack-gatk | SNP | ti | segdup | het | 97.5937 | 99.8088 | 95.4748 | 94.2828 | 12007 | 23 | 12005 | 569 | 5 | 0.8787 | |
| jlack-gatk | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8488 | 99.8809 | 99.8167 | 61.3691 | 10898 | 13 | 10894 | 20 | 5 | 25.0000 | |
| jlack-gatk | SNP | tv | map_l100_m0_e0 | homalt | 99.0571 | 98.3359 | 99.7889 | 62.7592 | 3782 | 64 | 3782 | 8 | 5 | 62.5000 | |
| jlack-gatk | SNP | tv | map_l125_m0_e0 | homalt | 98.7279 | 97.8388 | 99.6332 | 70.1233 | 2173 | 48 | 2173 | 8 | 5 | 62.5000 | |
| jlack-gatk | SNP | tv | map_l250_m0_e0 | het | 86.9976 | 96.5035 | 79.1966 | 96.2107 | 552 | 20 | 552 | 145 | 5 | 3.4483 | |
| jlack-gatk | SNP | tv | map_l250_m1_e0 | homalt | 98.5303 | 97.8972 | 99.1716 | 86.3357 | 838 | 18 | 838 | 7 | 5 | 71.4286 | |
| jlack-gatk | SNP | tv | map_l250_m2_e0 | homalt | 98.6581 | 98.0790 | 99.2441 | 87.2434 | 919 | 18 | 919 | 7 | 5 | 71.4286 | |
| jlack-gatk | SNP | tv | map_l250_m2_e1 | homalt | 98.6709 | 98.0973 | 99.2513 | 87.3083 | 928 | 18 | 928 | 7 | 5 | 71.4286 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 90.6149 | 83.1470 | 99.5567 | 28.0153 | 1041 | 211 | 1123 | 5 | 5 | 100.0000 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8263 | 99.7261 | 99.9268 | 57.6141 | 16384 | 45 | 16382 | 12 | 5 | 41.6667 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.4857 | 99.1089 | 99.8653 | 46.8501 | 6673 | 60 | 6673 | 9 | 5 | 55.5556 | |
| jli-custom | INDEL | * | map_l100_m0_e0 | het | 97.8452 | 97.8452 | 97.8452 | 85.1642 | 999 | 22 | 999 | 22 | 5 | 22.7273 | |
| jli-custom | INDEL | * | map_l100_m0_e0 | homalt | 98.6275 | 98.8212 | 98.4344 | 83.3605 | 503 | 6 | 503 | 8 | 5 | 62.5000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 79.4194 | 70.3704 | 91.1392 | 75.5418 | 95 | 40 | 72 | 7 | 5 | 71.4286 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9263 | 99.9017 | 99.9509 | 53.9245 | 10168 | 10 | 10168 | 5 | 5 | 100.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | map_siren | * | 99.3769 | 99.3199 | 99.4339 | 78.1455 | 3505 | 24 | 3513 | 20 | 5 | 25.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | * | hetalt | 96.0725 | 92.6597 | 99.7463 | 58.0281 | 1944 | 154 | 1966 | 5 | 5 | 100.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | HG002complexvar | homalt | 99.0385 | 100.0000 | 98.0952 | 69.9140 | 309 | 0 | 309 | 6 | 5 | 83.3333 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.2529 | 100.0000 | 89.1304 | 87.2928 | 41 | 0 | 41 | 5 | 5 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.6246 | 94.1088 | 97.1901 | 77.6009 | 623 | 39 | 588 | 17 | 5 | 29.4118 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.5799 | 90.9722 | 96.3415 | 79.3277 | 262 | 26 | 237 | 9 | 5 | 55.5556 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.0769 | 100.0000 | 96.2264 | 77.1879 | 153 | 0 | 153 | 6 | 5 | 83.3333 | |
| hfeng-pmm3 | SNP | * | HG002compoundhet | het | 96.0659 | 92.5730 | 99.8327 | 43.9121 | 13125 | 1053 | 13125 | 22 | 5 | 22.7273 | |
| hfeng-pmm3 | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5415 | 97.2452 | 99.8728 | 66.2892 | 9425 | 267 | 9425 | 12 | 5 | 41.6667 | |
| hfeng-pmm3 | SNP | * | map_l250_m0_e0 | homalt | 98.8124 | 99.2051 | 98.4227 | 92.6442 | 624 | 5 | 624 | 10 | 5 | 50.0000 | |
| hfeng-pmm3 | SNP | ti | HG002compoundhet | homalt | 99.9256 | 99.9189 | 99.9324 | 30.4123 | 7388 | 6 | 7388 | 5 | 5 | 100.0000 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.8678 | 98.1204 | 99.6266 | 68.0485 | 19211 | 368 | 19212 | 72 | 5 | 6.9444 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.8678 | 98.1204 | 99.6266 | 68.0485 | 19211 | 368 | 19212 | 72 | 5 | 6.9444 | |
| hfeng-pmm3 | SNP | ti | map_l125_m0_e0 | homalt | 99.6659 | 99.6437 | 99.6881 | 69.8765 | 4475 | 16 | 4475 | 14 | 5 | 35.7143 | |