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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
18151-18200 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | INDEL | D16_PLUS | HG002compoundhet | hetalt | 94.9583 | 90.9232 | 99.3682 | 22.2073 | 1753 | 175 | 1730 | 11 | 11 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.7242 | 88.2707 | 97.6510 | 77.3039 | 587 | 78 | 582 | 14 | 11 | 78.5714 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 91.3465 | 85.0256 | 98.6826 | 42.3343 | 829 | 146 | 824 | 11 | 11 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 90.6524 | 84.2181 | 98.1513 | 37.9562 | 587 | 110 | 584 | 11 | 11 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.2631 | 94.2205 | 98.3962 | 48.3858 | 1239 | 76 | 1227 | 20 | 11 | 55.0000 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | HG002complexvar | homalt | 95.1273 | 94.1748 | 96.0993 | 53.7705 | 291 | 18 | 271 | 11 | 11 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | HG002complexvar | hetalt | 97.3210 | 95.3071 | 99.4220 | 76.8604 | 1645 | 81 | 1892 | 11 | 11 | 100.0000 | |
| jli-custom | SNP | ti | map_l100_m1_e0 | homalt | 99.7965 | 99.6548 | 99.9386 | 56.4067 | 17898 | 62 | 17898 | 11 | 11 | 100.0000 | |
| jli-custom | SNP | ti | map_l100_m2_e0 | homalt | 99.8004 | 99.6614 | 99.9398 | 59.0453 | 18247 | 62 | 18247 | 11 | 11 | 100.0000 | |
| jli-custom | SNP | ti | map_l100_m2_e1 | homalt | 99.7997 | 99.6593 | 99.9404 | 59.0260 | 18431 | 63 | 18431 | 11 | 11 | 100.0000 | |
| jli-custom | SNP | tv | HG002complexvar | homalt | 99.9542 | 99.9254 | 99.9832 | 22.8543 | 95040 | 71 | 95029 | 16 | 11 | 68.7500 | |
| jli-custom | SNP | tv | map_l250_m1_e0 | * | 97.9966 | 97.0155 | 98.9977 | 85.0101 | 2568 | 79 | 2568 | 26 | 11 | 42.3077 | |
| jmaeng-gatk | INDEL | * | map_l125_m1_e0 | * | 96.6159 | 98.1016 | 95.1746 | 90.8498 | 2067 | 40 | 2071 | 105 | 11 | 10.4762 | |
| jmaeng-gatk | INDEL | * | map_l125_m2_e0 | * | 96.6195 | 98.1330 | 95.1520 | 91.4584 | 2155 | 41 | 2159 | 110 | 11 | 10.0000 | |
| jmaeng-gatk | INDEL | * | map_l125_m2_e1 | * | 96.6186 | 98.1124 | 95.1697 | 91.5159 | 2183 | 42 | 2187 | 111 | 11 | 9.9099 | |
| jmaeng-gatk | INDEL | * | segdup | * | 96.3424 | 98.8654 | 93.9450 | 95.7742 | 2527 | 29 | 2529 | 163 | 11 | 6.7485 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.8366 | 99.9727 | 99.7008 | 51.3048 | 3665 | 1 | 3665 | 11 | 11 | 100.0000 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.3125 | 100.0000 | 91.0448 | 86.9776 | 122 | 0 | 122 | 12 | 11 | 91.6667 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 94.9273 | 92.5764 | 97.4006 | 82.2668 | 636 | 51 | 637 | 17 | 11 | 64.7059 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.6425 | 98.1293 | 99.1611 | 76.9773 | 2413 | 46 | 2364 | 20 | 11 | 55.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.1541 | 94.6964 | 99.7428 | 58.3391 | 5428 | 304 | 5429 | 14 | 11 | 78.5714 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.1487 | 97.4632 | 98.8439 | 76.5004 | 1921 | 50 | 1881 | 22 | 11 | 50.0000 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.1487 | 97.4632 | 98.8439 | 76.5004 | 1921 | 50 | 1881 | 22 | 11 | 50.0000 | |
| jmaeng-gatk | SNP | * | HG002compoundhet | homalt | 99.4551 | 99.0262 | 99.8877 | 35.0471 | 10677 | 105 | 10676 | 12 | 11 | 91.6667 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 99.1693 | 98.8590 | 99.4815 | 88.1277 | 2686 | 31 | 2686 | 14 | 11 | 78.5714 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.3451 | 99.1719 | 99.5189 | 81.7458 | 6826 | 57 | 6826 | 33 | 11 | 33.3333 | |
| jmaeng-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.7273 | 99.7114 | 99.7433 | 70.7941 | 6218 | 18 | 6218 | 16 | 11 | 68.7500 | |
| jmaeng-gatk | INDEL | D1_5 | map_siren | * | 98.0661 | 98.9799 | 97.1690 | 84.7576 | 3493 | 36 | 3501 | 102 | 10 | 9.8039 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.9768 | 87.2358 | 99.5265 | 30.0431 | 2064 | 302 | 2102 | 10 | 10 | 100.0000 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.0963 | 91.3481 | 97.0149 | 75.7623 | 454 | 43 | 455 | 14 | 10 | 71.4286 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.1199 | 93.3333 | 96.9762 | 82.0124 | 448 | 32 | 449 | 14 | 10 | 71.4286 | |
| 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 | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 96.5300 | 100.0000 | 93.2927 | 77.6871 | 153 | 0 | 153 | 11 | 10 | 90.9091 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 99.0341 | 98.8095 | 99.2597 | 89.1343 | 1743 | 21 | 1743 | 13 | 10 | 76.9231 | |
| jmaeng-gatk | SNP | * | map_l250_m2_e0 | * | 70.5188 | 55.3329 | 97.1931 | 96.2932 | 4363 | 3522 | 4363 | 126 | 10 | 7.9365 | |
| jmaeng-gatk | SNP | * | map_l250_m2_e1 | * | 70.7185 | 55.5778 | 97.1973 | 96.3060 | 4439 | 3548 | 4439 | 128 | 10 | 7.8125 | |
| jmaeng-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.7157 | 99.7174 | 99.7139 | 56.2929 | 27880 | 79 | 27879 | 80 | 10 | 12.5000 | |
| jmaeng-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.1507 | 99.0803 | 97.2383 | 83.3124 | 9049 | 84 | 9049 | 257 | 10 | 3.8911 | |
| jmaeng-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.1507 | 99.0803 | 97.2383 | 83.3124 | 9049 | 84 | 9049 | 257 | 10 | 3.8911 | |
| jmaeng-gatk | SNP | tv | map_l100_m0_e0 | het | 84.7992 | 76.2808 | 95.4593 | 88.1483 | 5509 | 1713 | 5508 | 262 | 10 | 3.8168 | |
| jpowers-varprowl | INDEL | * | map_l250_m1_e0 | het | 90.4255 | 89.4737 | 91.3978 | 96.9623 | 170 | 20 | 170 | 16 | 10 | 62.5000 | |
| jpowers-varprowl | INDEL | * | map_l250_m2_e0 | het | 91.1271 | 90.4762 | 91.7874 | 97.0352 | 190 | 20 | 190 | 17 | 10 | 58.8235 | |
| jpowers-varprowl | INDEL | * | map_l250_m2_e1 | het | 91.1695 | 90.5213 | 91.8269 | 97.1006 | 191 | 20 | 191 | 17 | 10 | 58.8235 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 72.0930 | 70.4545 | 73.8095 | 97.7600 | 31 | 13 | 31 | 11 | 10 | 90.9091 | |
| jpowers-varprowl | INDEL | D1_5 | func_cds | * | 93.0818 | 93.0818 | 93.0818 | 35.6275 | 148 | 11 | 148 | 11 | 10 | 90.9091 | |
| jpowers-varprowl | INDEL | D1_5 | func_cds | het | 93.3333 | 98.8235 | 88.4211 | 41.7178 | 84 | 1 | 84 | 11 | 10 | 90.9091 | |
| jpowers-varprowl | INDEL | D1_5 | map_l125_m0_e0 | * | 94.8537 | 94.7581 | 94.9495 | 88.5760 | 470 | 26 | 470 | 25 | 10 | 40.0000 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 13.3333 | 100.0000 | 7.1429 | 89.5522 | 1 | 0 | 1 | 13 | 10 | 76.9231 | |
| jpowers-varprowl | INDEL | I1_5 | map_l100_m0_e0 | het | 93.4783 | 92.3313 | 94.6541 | 88.2916 | 301 | 25 | 301 | 17 | 10 | 58.8235 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.8896 | 99.2565 | 98.5255 | 64.2421 | 2937 | 22 | 2940 | 44 | 10 | 22.7273 | |