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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
43651-43700 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 75.1220 | 60.6299 | 98.7179 | 63.3803 | 77 | 50 | 77 | 1 | 1 | 100.0000 | |
| gduggal-snapfb | SNP | * | HG002compoundhet | het | 75.1230 | 97.0518 | 61.2774 | 50.8228 | 13760 | 418 | 14027 | 8864 | 298 | 3.3619 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 75.1306 | 62.9044 | 93.2559 | 77.8634 | 1672 | 986 | 1687 | 122 | 15 | 12.2951 | |
| anovak-vg | SNP | * | map_l250_m2_e0 | * | 75.1311 | 81.7121 | 69.5312 | 91.5463 | 6443 | 1442 | 6392 | 2801 | 650 | 23.2060 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 75.1328 | 73.0570 | 77.3300 | 87.4921 | 282 | 104 | 307 | 90 | 26 | 28.8889 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 75.1358 | 70.1613 | 80.8696 | 87.6477 | 87 | 37 | 93 | 22 | 0 | 0.0000 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 75.1438 | 70.5882 | 80.3279 | 96.6630 | 48 | 20 | 49 | 12 | 11 | 91.6667 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 75.1472 | 60.1887 | 100.0000 | 53.6122 | 319 | 211 | 122 | 0 | 0 | ||
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 75.1496 | 77.5758 | 72.8707 | 49.6025 | 256 | 74 | 231 | 86 | 83 | 96.5116 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 75.1515 | 60.1942 | 100.0000 | 58.4718 | 124 | 82 | 125 | 0 | 0 | ||
| ckim-dragen | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 75.1515 | 60.1942 | 100.0000 | 60.6918 | 124 | 82 | 125 | 0 | 0 | ||
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 75.1577 | 77.7747 | 72.7110 | 36.3946 | 2845 | 813 | 4074 | 1529 | 1142 | 74.6893 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 75.1664 | 60.6286 | 98.8753 | 39.2261 | 5633 | 3658 | 5187 | 59 | 47 | 79.6610 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 75.1664 | 60.6286 | 98.8753 | 39.2261 | 5633 | 3658 | 5187 | 59 | 47 | 79.6610 | |
| gduggal-bwaplat | SNP | * | map_l125_m2_e0 | * | 75.1671 | 60.4306 | 99.4087 | 87.7400 | 28235 | 18488 | 28242 | 168 | 47 | 27.9762 | |
| gduggal-bwaplat | INDEL | * | map_l150_m2_e1 | het | 75.1678 | 60.6061 | 98.9399 | 96.4527 | 560 | 364 | 560 | 6 | 1 | 16.6667 | |
| gduggal-bwaplat | INDEL | D6_15 | map_l100_m2_e1 | * | 75.1678 | 61.0909 | 97.6744 | 94.2049 | 168 | 107 | 168 | 4 | 1 | 25.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 75.1699 | 81.7568 | 69.5652 | 72.8346 | 121 | 27 | 96 | 42 | 42 | 100.0000 | |
| ckim-vqsr | SNP | tv | map_l100_m2_e0 | * | 75.1758 | 60.6200 | 98.9306 | 85.6823 | 15175 | 9858 | 15172 | 164 | 1 | 0.6098 | |
| gduggal-bwaplat | SNP | ti | map_l150_m2_e0 | het | 75.1762 | 60.5388 | 99.1490 | 91.7226 | 7798 | 5083 | 7806 | 67 | 22 | 32.8358 | |
| gduggal-bwaplat | INDEL | D1_5 | map_l100_m0_e0 | * | 75.1793 | 60.7184 | 98.6817 | 93.9453 | 524 | 339 | 524 | 7 | 1 | 14.2857 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 75.1880 | 60.2410 | 100.0000 | 32.9412 | 50 | 33 | 57 | 0 | 0 | ||
| qzeng-custom | INDEL | I6_15 | map_l125_m2_e0 | homalt | 75.1899 | 73.3333 | 77.1429 | 83.7209 | 11 | 4 | 27 | 8 | 0 | 0.0000 | |
| qzeng-custom | INDEL | I6_15 | map_l125_m2_e1 | homalt | 75.1899 | 73.3333 | 77.1429 | 84.1629 | 11 | 4 | 27 | 8 | 0 | 0.0000 | |
| gduggal-bwavard | INDEL | D16_PLUS | HG002complexvar | * | 75.2016 | 72.3676 | 78.2666 | 64.6225 | 1189 | 454 | 1192 | 331 | 268 | 80.9668 | |
| gduggal-snapfb | INDEL | * | map_l125_m2_e1 | hetalt | 75.2098 | 67.4419 | 85.0000 | 95.3271 | 29 | 14 | 17 | 3 | 1 | 33.3333 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 75.2099 | 92.3698 | 63.4269 | 72.4538 | 1259 | 104 | 1266 | 730 | 77 | 10.5479 | |
| gduggal-bwaplat | INDEL | D6_15 | map_l150_m1_e0 | * | 75.2137 | 60.2740 | 100.0000 | 96.7953 | 44 | 29 | 44 | 0 | 0 | ||
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 75.2137 | 86.2745 | 66.6667 | 57.1429 | 44 | 7 | 2 | 1 | 1 | 100.0000 | |
| anovak-vg | SNP | * | map_l250_m2_e1 | * | 75.2143 | 81.7954 | 69.6133 | 91.5868 | 6533 | 1454 | 6481 | 2829 | 654 | 23.1177 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 75.2156 | 61.3260 | 97.2393 | 52.0588 | 222 | 140 | 634 | 18 | 18 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 75.2215 | 62.0370 | 95.5224 | 69.6833 | 67 | 41 | 64 | 3 | 2 | 66.6667 | |
| ckim-isaac | SNP | ti | map_l150_m1_e0 | het | 75.2265 | 60.4123 | 99.6666 | 78.7514 | 7473 | 4897 | 7473 | 25 | 2 | 8.0000 | |
| gduggal-bwafb | INDEL | * | map_l100_m1_e0 | hetalt | 75.2274 | 61.2903 | 97.3684 | 92.9630 | 76 | 48 | 37 | 1 | 1 | 100.0000 | |
| mlin-fermikit | INDEL | D6_15 | map_l100_m2_e0 | * | 75.2386 | 70.0758 | 81.2227 | 82.7430 | 185 | 79 | 186 | 43 | 33 | 76.7442 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 75.2475 | 66.6667 | 86.3636 | 89.8148 | 18 | 9 | 19 | 3 | 1 | 33.3333 | |
| ckim-isaac | SNP | ti | map_l125_m2_e0 | * | 75.2532 | 60.4006 | 99.7925 | 72.3144 | 18276 | 11982 | 18276 | 38 | 7 | 18.4211 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 75.2576 | 62.8247 | 93.8257 | 69.9746 | 774 | 458 | 775 | 51 | 20 | 39.2157 | |
| gduggal-bwavard | INDEL | * | map_l250_m0_e0 | * | 75.2577 | 93.5897 | 62.9310 | 97.7692 | 73 | 5 | 73 | 43 | 2 | 4.6512 | |
| ckim-vqsr | SNP | * | map_l125_m0_e0 | het | 75.2621 | 60.9365 | 98.3935 | 91.9254 | 7717 | 4947 | 7717 | 126 | 0 | 0.0000 | |
| gduggal-snapfb | INDEL | D6_15 | HG002complexvar | het | 75.2635 | 62.8205 | 93.8532 | 43.4007 | 1960 | 1160 | 2443 | 160 | 143 | 89.3750 | |
| gduggal-snapplat | INDEL | * | HG002complexvar | * | 75.2674 | 67.2243 | 85.4968 | 64.1998 | 51721 | 25217 | 55926 | 9487 | 1463 | 15.4211 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 75.2713 | 61.0778 | 98.0583 | 75.8782 | 102 | 65 | 101 | 2 | 2 | 100.0000 | |
| ghariani-varprowl | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 75.2746 | 87.2549 | 66.1871 | 95.4411 | 89 | 13 | 92 | 47 | 3 | 6.3830 | |
| gduggal-bwaplat | SNP | ti | map_l150_m2_e1 | het | 75.2791 | 60.6685 | 99.1595 | 91.7406 | 7896 | 5119 | 7904 | 67 | 22 | 32.8358 | |
| ckim-gatk | SNP | tv | map_l100_m0_e0 | homalt | 75.2796 | 60.3744 | 99.9570 | 73.4271 | 2322 | 1524 | 2322 | 1 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 75.2837 | 62.1359 | 95.4887 | 76.4184 | 128 | 78 | 127 | 6 | 4 | 66.6667 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 75.2854 | 64.8571 | 89.7098 | 61.7172 | 681 | 369 | 680 | 78 | 71 | 91.0256 | |
| gduggal-snapplat | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 75.2906 | 65.9666 | 87.6843 | 78.0956 | 20292 | 10469 | 23253 | 3266 | 1977 | 60.5328 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 75.2916 | 86.8093 | 66.4721 | 57.3739 | 6410 | 974 | 6834 | 3447 | 1755 | 50.9138 | |