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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
12051-12100 / 86044 show all | |||||||||||||||
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.4525 | 98.8280 | 98.0798 | 67.6014 | 30778 | 365 | 31005 | 607 | 33 | 5.4366 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.4525 | 98.8280 | 98.0798 | 67.6014 | 30778 | 365 | 31005 | 607 | 33 | 5.4366 | |
| ndellapenna-hhga | INDEL | I1_5 | HG002complexvar | het | 98.8489 | 98.2847 | 99.4197 | 54.6026 | 17877 | 312 | 17818 | 104 | 33 | 31.7308 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 88.8393 | 94.3128 | 83.9662 | 66.8067 | 199 | 12 | 199 | 38 | 33 | 86.8421 | |
| ndellapenna-hhga | SNP | ti | segdup | * | 99.5651 | 99.6059 | 99.5244 | 88.6856 | 19460 | 77 | 19460 | 93 | 33 | 35.4839 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 81.3930 | 81.0811 | 81.7073 | 53.8028 | 180 | 42 | 268 | 60 | 33 | 55.0000 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 95.2685 | 95.4338 | 95.1039 | 78.5282 | 836 | 40 | 641 | 33 | 33 | 100.0000 | |
| jli-custom | INDEL | D6_15 | HG002compoundhet | hetalt | 97.6428 | 95.7919 | 99.5667 | 24.6880 | 7808 | 343 | 7812 | 34 | 33 | 97.0588 | |
| jpowers-varprowl | INDEL | D16_PLUS | HG002complexvar | homalt | 80.0982 | 75.0865 | 85.8268 | 71.4607 | 217 | 72 | 218 | 36 | 33 | 91.6667 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.7472 | 94.1475 | 99.4946 | 23.8423 | 6483 | 403 | 6496 | 33 | 33 | 100.0000 | |
| jmaeng-gatk | SNP | ti | map_l150_m1_e0 | het | 84.7465 | 75.2789 | 96.9381 | 89.5763 | 9312 | 3058 | 9308 | 294 | 33 | 11.2245 | |
| jmaeng-gatk | SNP | ti | map_l150_m2_e0 | het | 85.2876 | 76.1276 | 96.9535 | 90.1394 | 9806 | 3075 | 9802 | 308 | 33 | 10.7143 | |
| jmaeng-gatk | SNP | ti | map_l150_m2_e1 | het | 85.3846 | 76.2889 | 96.9428 | 90.1640 | 9929 | 3086 | 9925 | 313 | 33 | 10.5431 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.5234 | 99.1268 | 97.9273 | 65.2174 | 6130 | 54 | 6142 | 130 | 33 | 25.3846 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 79.9744 | 90.9326 | 71.3733 | 92.8433 | 351 | 35 | 369 | 148 | 33 | 22.2973 | |
| jpowers-varprowl | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.2548 | 98.6087 | 97.9035 | 45.6956 | 3402 | 48 | 3409 | 73 | 33 | 45.2055 | |
| jpowers-varprowl | SNP | tv | map_l250_m1_e0 | * | 94.0667 | 94.3332 | 93.8017 | 91.6023 | 2497 | 150 | 2497 | 165 | 33 | 20.0000 | |
| jpowers-varprowl | SNP | tv | segdup | * | 97.6941 | 99.0272 | 96.3964 | 93.1340 | 8449 | 83 | 8453 | 316 | 33 | 10.4430 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.9739 | 98.2672 | 99.6909 | 53.0163 | 11285 | 199 | 11289 | 35 | 33 | 94.2857 | |
| jli-custom | SNP | ti | map_l125_m1_e0 | het | 99.1158 | 98.8065 | 99.4270 | 68.8246 | 18048 | 218 | 18046 | 104 | 33 | 31.7308 | |
| jli-custom | SNP | ti | map_l125_m2_e0 | het | 99.1286 | 98.8398 | 99.4191 | 70.5575 | 18657 | 219 | 18655 | 109 | 33 | 30.2752 | |
| jli-custom | SNP | ti | map_l125_m2_e1 | het | 99.1383 | 98.8526 | 99.4256 | 70.6228 | 18868 | 219 | 18866 | 109 | 33 | 30.2752 | |
| jli-custom | SNP | tv | HG002complexvar | * | 99.9252 | 99.8822 | 99.9683 | 21.9781 | 245862 | 290 | 245791 | 78 | 33 | 42.3077 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.7927 | 97.6562 | 97.9295 | 69.6398 | 1750 | 42 | 1750 | 37 | 33 | 89.1892 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2071 | 90.0993 | 98.7075 | 49.5392 | 3540 | 389 | 3513 | 46 | 33 | 71.7391 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 94.1097 | 95.4459 | 92.8105 | 80.6084 | 503 | 24 | 426 | 33 | 33 | 100.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.7679 | 94.4049 | 99.2523 | 24.5186 | 4505 | 267 | 4513 | 34 | 33 | 97.0588 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.7353 | 98.9667 | 98.5050 | 75.1773 | 2969 | 31 | 2965 | 45 | 33 | 73.3333 | |
| astatham-gatk | SNP | * | map_l100_m1_e0 | het | 86.7442 | 76.7367 | 99.7535 | 74.2815 | 34807 | 10552 | 34796 | 86 | 33 | 38.3721 | |
| astatham-gatk | SNP | * | map_l100_m2_e0 | het | 86.8923 | 76.9650 | 99.7597 | 75.4072 | 35711 | 10688 | 35700 | 86 | 33 | 38.3721 | |
| astatham-gatk | SNP | * | map_l100_m2_e1 | het | 86.9224 | 77.0139 | 99.7569 | 75.4083 | 36118 | 10780 | 36107 | 88 | 33 | 37.5000 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.8171 | 100.0000 | 90.1449 | 70.2842 | 311 | 0 | 311 | 34 | 33 | 97.0588 | |
| bgallagher-sentieon | SNP | ti | map_l125_m1_e0 | het | 99.0798 | 99.3430 | 98.8180 | 74.4018 | 18146 | 120 | 18142 | 217 | 33 | 15.2074 | |
| bgallagher-sentieon | SNP | ti | map_l125_m2_e0 | het | 99.0858 | 99.3537 | 98.8194 | 75.6140 | 18754 | 122 | 18750 | 224 | 33 | 14.7321 | |
| bgallagher-sentieon | SNP | ti | map_l125_m2_e1 | het | 99.0933 | 99.3608 | 98.8273 | 75.6520 | 18965 | 122 | 18961 | 225 | 33 | 14.6667 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.7159 | 97.8795 | 97.5528 | 69.2597 | 1754 | 38 | 1754 | 44 | 33 | 75.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.8780 | 94.3944 | 99.4959 | 25.6896 | 6500 | 386 | 6513 | 33 | 33 | 100.0000 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.6730 | 92.4844 | 99.0893 | 41.0583 | 3261 | 265 | 3808 | 35 | 33 | 94.2857 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.6730 | 92.4844 | 99.0893 | 41.0583 | 3261 | 265 | 3808 | 35 | 33 | 94.2857 | |
| asubramanian-gatk | SNP | * | map_siren | het | 78.4554 | 64.6317 | 99.8014 | 73.5808 | 58809 | 32182 | 58800 | 117 | 33 | 28.2051 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 34.8293 | 37.7778 | 32.3077 | 48.0000 | 17 | 28 | 21 | 44 | 33 | 75.0000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.3908 | 95.3819 | 99.4860 | 25.9321 | 6568 | 318 | 6581 | 34 | 33 | 97.0588 | |
| astatham-gatk | INDEL | D6_15 | HG002compoundhet | hetalt | 97.1670 | 94.8841 | 99.5625 | 24.4483 | 7734 | 417 | 7738 | 34 | 33 | 97.0588 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.9663 | 95.1890 | 98.8113 | 52.9502 | 3324 | 168 | 3325 | 40 | 33 | 82.5000 | |
| anovak-vg | INDEL | I1_5 | map_l250_m2_e0 | * | 59.4374 | 62.8319 | 56.3910 | 96.6841 | 71 | 42 | 75 | 58 | 33 | 56.8966 | |
| anovak-vg | INDEL | I1_5 | map_l250_m2_e1 | * | 59.7641 | 63.1579 | 56.7164 | 96.7476 | 72 | 42 | 76 | 58 | 33 | 56.8966 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 97.9828 | 97.6625 | 98.3051 | 30.8535 | 2674 | 64 | 2668 | 46 | 33 | 71.7391 | |
| anovak-vg | SNP | * | map_l125_m0_e0 | homalt | 85.5602 | 75.1937 | 99.2421 | 70.8421 | 5047 | 1665 | 4976 | 38 | 33 | 86.8421 | |
| anovak-vg | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.4369 | 98.7908 | 98.0854 | 58.8485 | 3840 | 47 | 3996 | 78 | 33 | 42.3077 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.7461 | 88.4908 | 97.4313 | 66.6799 | 1630 | 212 | 1631 | 43 | 33 | 76.7442 | |