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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
22001-22050 / 86044 show all | |||||||||||||||
| qzeng-custom | SNP | tv | func_cds | het | 99.5488 | 99.6613 | 99.4365 | 40.8444 | 2648 | 9 | 2647 | 15 | 0 | 0.0000 | |
| raldana-dualsentieon | INDEL | * | map_l250_m1_e0 | het | 93.2292 | 94.2105 | 92.2680 | 95.0218 | 179 | 11 | 179 | 15 | 1 | 6.6667 | |
| raldana-dualsentieon | INDEL | * | map_l250_m2_e0 | het | 93.8679 | 94.7619 | 92.9907 | 95.2339 | 199 | 11 | 199 | 15 | 1 | 6.6667 | |
| raldana-dualsentieon | INDEL | * | map_l250_m2_e1 | het | 93.8967 | 94.7867 | 93.0233 | 95.3524 | 200 | 11 | 200 | 15 | 1 | 6.6667 | |
| ltrigg-rtg2 | INDEL | D1_5 | map_l100_m2_e1 | * | 98.0955 | 97.0088 | 99.2068 | 77.5974 | 1881 | 58 | 1876 | 15 | 2 | 13.3333 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.6844 | 90.6909 | 99.0458 | 31.4136 | 1549 | 159 | 1557 | 15 | 15 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | HG002compoundhet | hetalt | 98.4111 | 97.0028 | 99.8609 | 64.1248 | 10842 | 335 | 10768 | 15 | 15 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.3471 | 97.3466 | 99.3684 | 59.4294 | 2348 | 64 | 2360 | 15 | 9 | 60.0000 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.9665 | 97.1234 | 98.8245 | 57.1668 | 1283 | 38 | 1261 | 15 | 8 | 53.3333 | |
| ltrigg-rtg2 | SNP | * | map_l150_m0_e0 | het | 96.8156 | 94.0050 | 99.7994 | 59.7632 | 7464 | 476 | 7461 | 15 | 0 | 0.0000 | |
| qzeng-custom | INDEL | D16_PLUS | func_cds | * | 61.5385 | 100.0000 | 44.4444 | 64.4737 | 12 | 0 | 12 | 15 | 0 | 0.0000 | |
| qzeng-custom | INDEL | D16_PLUS | map_l150_m2_e1 | het | 68.9655 | 93.7500 | 54.5455 | 96.5300 | 15 | 1 | 18 | 15 | 0 | 0.0000 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.7242 | 99.5972 | 99.8516 | 52.5270 | 10137 | 41 | 10092 | 15 | 11 | 73.3333 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 93.2079 | 95.2756 | 91.2281 | 74.8899 | 121 | 6 | 156 | 15 | 5 | 33.3333 | |
| qzeng-custom | INDEL | D6_15 | map_l125_m1_e0 | het | 83.2909 | 81.2500 | 85.4369 | 92.7821 | 52 | 12 | 88 | 15 | 2 | 13.3333 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 0.0000 | 0.0000 | 95.5752 | 0 | 0 | 0 | 15 | 0 | 0.0000 | ||
| qzeng-custom | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 93.3984 | 91.5194 | 95.3560 | 62.7021 | 259 | 24 | 308 | 15 | 12 | 80.0000 | |
| qzeng-custom | INDEL | I1_5 | segdup | het | 97.4851 | 97.5836 | 97.3868 | 95.7292 | 525 | 13 | 559 | 15 | 2 | 13.3333 | |
| mlin-fermikit | INDEL | D6_15 | HG002complexvar | hetalt | 87.9228 | 79.5656 | 98.2415 | 48.4281 | 806 | 207 | 838 | 15 | 15 | 100.0000 | |
| mlin-fermikit | INDEL | I16_PLUS | HG002compoundhet | hetalt | 66.4170 | 50.0717 | 98.6059 | 45.0179 | 1048 | 1045 | 1061 | 15 | 14 | 93.3333 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 97.8956 | 97.3822 | 98.4144 | 74.9934 | 930 | 25 | 931 | 15 | 13 | 86.6667 | |
| mlin-fermikit | SNP | * | func_cds | het | 99.3878 | 98.9159 | 99.8643 | 18.4193 | 11040 | 121 | 11040 | 15 | 0 | 0.0000 | |
| mlin-fermikit | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 76.9887 | 88.5714 | 68.0851 | 93.5351 | 31 | 4 | 32 | 15 | 14 | 93.3333 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.2767 | 87.0680 | 98.1481 | 43.3170 | 781 | 116 | 795 | 15 | 13 | 86.6667 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.0761 | 97.2854 | 98.8798 | 74.4855 | 1326 | 37 | 1324 | 15 | 8 | 53.3333 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 80.9816 | 80.4878 | 81.4815 | 72.4490 | 66 | 16 | 66 | 15 | 14 | 93.3333 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 92.8087 | 91.4498 | 94.2085 | 69.3853 | 246 | 23 | 244 | 15 | 7 | 46.6667 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 89.3491 | 89.2617 | 89.4366 | 73.6549 | 133 | 16 | 127 | 15 | 9 | 60.0000 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5635 | 99.5014 | 99.6257 | 47.9205 | 3991 | 20 | 3992 | 15 | 4 | 26.6667 | |
| ndellapenna-hhga | SNP | ti | map_l100_m2_e0 | homalt | 99.7949 | 99.6723 | 99.9179 | 61.7916 | 18249 | 60 | 18249 | 15 | 15 | 100.0000 | |
| ndellapenna-hhga | SNP | ti | map_l100_m2_e1 | homalt | 99.7970 | 99.6756 | 99.9187 | 61.7788 | 18434 | 60 | 18434 | 15 | 15 | 100.0000 | |
| ndellapenna-hhga | SNP | ti | map_l250_m2_e1 | het | 97.7791 | 96.0897 | 99.5290 | 88.4572 | 3170 | 129 | 3170 | 15 | 6 | 40.0000 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 96.3257 | 95.6607 | 97.0000 | 82.2127 | 485 | 22 | 485 | 15 | 15 | 100.0000 | |
| ndellapenna-hhga | SNP | tv | map_l250_m1_e0 | het | 97.1755 | 95.2994 | 99.1269 | 86.3845 | 1703 | 84 | 1703 | 15 | 8 | 53.3333 | |
| qzeng-custom | INDEL | C16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 0.0000 | 0.0000 | 11.7647 | 95.0292 | 0 | 0 | 2 | 15 | 0 | 0.0000 | |
| qzeng-custom | INDEL | C16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 0.0000 | 0.0000 | 11.7647 | 95.0292 | 0 | 0 | 2 | 15 | 0 | 0.0000 | |
| qzeng-custom | INDEL | C16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 0.0000 | 0.0000 | 16.6667 | 93.4307 | 0 | 0 | 3 | 15 | 0 | 0.0000 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5944 | 99.7950 | 99.3947 | 49.7872 | 2434 | 5 | 2463 | 15 | 0 | 0.0000 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.4692 | 99.8734 | 99.0683 | 51.6226 | 1578 | 2 | 1595 | 15 | 0 | 0.0000 | |
| ltrigg-rtg2 | SNP | ti | map_l150_m1_e0 | het | 98.1622 | 96.5077 | 99.8745 | 59.1812 | 11938 | 432 | 11940 | 15 | 1 | 6.6667 | |
| ltrigg-rtg2 | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.5345 | 99.7661 | 99.3039 | 36.1103 | 2133 | 5 | 2140 | 15 | 2 | 13.3333 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 96.4384 | 95.9432 | 96.9388 | 58.1197 | 473 | 20 | 475 | 15 | 12 | 80.0000 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 97.8845 | 98.5348 | 97.2426 | 75.8758 | 538 | 8 | 529 | 15 | 15 | 100.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.4573 | 97.8921 | 99.0291 | 73.9064 | 1579 | 34 | 1530 | 15 | 10 | 66.6667 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.5281 | 99.6497 | 97.4315 | 67.4470 | 569 | 2 | 569 | 15 | 15 | 100.0000 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 62.0650 | 56.1404 | 69.3878 | 99.4106 | 32 | 25 | 34 | 15 | 8 | 53.3333 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 53.4400 | 37.6975 | 91.7582 | 47.5504 | 167 | 276 | 167 | 15 | 13 | 86.6667 | |
| jpowers-varprowl | INDEL | I6_15 | map_l100_m1_e0 | * | 67.0103 | 57.0175 | 81.2500 | 85.1852 | 65 | 49 | 65 | 15 | 15 | 100.0000 | |
| jpowers-varprowl | INDEL | I6_15 | map_l100_m2_e0 | * | 67.0051 | 56.8966 | 81.4815 | 86.4775 | 66 | 50 | 66 | 15 | 15 | 100.0000 | |
| jpowers-varprowl | INDEL | I6_15 | map_l100_m2_e1 | * | 67.0051 | 56.8966 | 81.4815 | 86.6776 | 66 | 50 | 66 | 15 | 15 | 100.0000 | |