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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
67201-67250 / 86044 show all | |||||||||||||||
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.1374 | 97.6583 | 98.6213 | 37.9185 | 2669 | 64 | 8083 | 113 | 105 | 92.9204 | |
| ciseli-custom | INDEL | D16_PLUS | map_l100_m2_e1 | * | 43.8881 | 34.0206 | 61.8182 | 89.1304 | 33 | 64 | 34 | 21 | 15 | 71.4286 | |
| ciseli-custom | INDEL | D1_5 | map_l125_m2_e0 | homalt | 81.6849 | 82.4176 | 80.9651 | 86.8337 | 300 | 64 | 302 | 71 | 59 | 83.0986 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 0.0000 | 64.2458 | 0.0000 | 0.0000 | 115 | 64 | 0 | 0 | 0 | ||
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.7052 | 90.8178 | 98.9404 | 37.4482 | 633 | 64 | 747 | 8 | 8 | 100.0000 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 64.7519 | 58.7097 | 72.1805 | 82.7048 | 91 | 64 | 96 | 37 | 36 | 97.2973 | |
| gduggal-bwavard | SNP | tv | func_cds | * | 99.0223 | 98.5358 | 99.5136 | 36.8583 | 4307 | 64 | 4296 | 21 | 9 | 42.8571 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 16.6415 | 14.6667 | 19.2308 | 69.7674 | 11 | 64 | 10 | 42 | 38 | 90.4762 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 68.4671 | 69.3780 | 67.5799 | 76.7516 | 145 | 64 | 148 | 71 | 49 | 69.0141 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 62.9688 | 47.5410 | 93.2203 | 73.6607 | 58 | 64 | 55 | 4 | 2 | 50.0000 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 92.5121 | 98.4899 | 87.2184 | 86.1606 | 4174 | 64 | 3910 | 573 | 37 | 6.4572 | |
| eyeh-varpipe | SNP | ti | map_l150_m2_e0 | het | 98.7657 | 99.5031 | 98.0391 | 80.4407 | 12817 | 64 | 12549 | 251 | 11 | 4.3825 | |
| eyeh-varpipe | SNP | ti | map_l150_m2_e1 | het | 98.7627 | 99.5083 | 98.0281 | 80.5176 | 12951 | 64 | 12677 | 255 | 11 | 4.3137 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 76.2290 | 62.1302 | 98.6047 | 43.8642 | 105 | 64 | 424 | 6 | 6 | 100.0000 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 82.2369 | 70.5069 | 98.6486 | 35.9307 | 153 | 64 | 146 | 2 | 2 | 100.0000 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 86.1668 | 94.2029 | 79.3939 | 87.5000 | 1040 | 64 | 1048 | 272 | 43 | 15.8088 | |
| gduggal-bwafb | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5732 | 99.3661 | 99.7812 | 63.9280 | 10033 | 64 | 10032 | 22 | 17 | 77.2727 | |
| gduggal-bwafb | SNP | tv | map_l150_m0_e0 | het | 97.3551 | 97.7489 | 96.9644 | 82.8486 | 2779 | 64 | 2779 | 87 | 20 | 22.9885 | |
| gduggal-bwaplat | INDEL | D16_PLUS | map_siren | * | 70.5357 | 55.2448 | 97.5309 | 95.0185 | 79 | 64 | 79 | 2 | 2 | 100.0000 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 85.8407 | 75.1938 | 100.0000 | 69.0590 | 194 | 64 | 194 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.9007 | 95.1331 | 98.7352 | 48.1982 | 1251 | 64 | 1249 | 16 | 11 | 68.7500 | |
| hfeng-pmm3 | SNP | * | map_siren | homalt | 99.9057 | 99.8840 | 99.9274 | 53.2388 | 55092 | 64 | 55083 | 40 | 22 | 55.0000 | |
| hfeng-pmm3 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.8359 | 98.0296 | 99.6557 | 67.1059 | 3184 | 64 | 3184 | 11 | 0 | 0.0000 | |
| 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_l150_m2_e1 | homalt | 99.1112 | 98.4519 | 99.7794 | 72.2800 | 4070 | 64 | 4070 | 9 | 6 | 66.6667 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.7925 | 97.6137 | 100.0000 | 42.7983 | 2618 | 64 | 2637 | 0 | 0 | ||
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.4824 | 96.4286 | 96.5363 | 69.2228 | 1728 | 64 | 1728 | 62 | 48 | 77.4194 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7712 | 99.7476 | 99.7949 | 55.7977 | 25295 | 64 | 25298 | 52 | 25 | 48.0769 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.8631 | 95.1331 | 98.6572 | 48.4108 | 1251 | 64 | 1249 | 17 | 12 | 70.5882 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.4894 | 96.4286 | 98.5739 | 66.0205 | 1728 | 64 | 1728 | 25 | 17 | 68.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.2475 | 95.8170 | 98.7214 | 83.8109 | 1466 | 64 | 1467 | 19 | 9 | 47.3684 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.2475 | 95.8170 | 98.7214 | 83.8109 | 1466 | 64 | 1467 | 19 | 9 | 47.3684 | |
| hfeng-pmm2 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.0002 | 96.8379 | 99.1907 | 64.6712 | 1960 | 64 | 1961 | 16 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.7158 | 99.7919 | 99.6397 | 70.7329 | 30697 | 64 | 30697 | 111 | 106 | 95.4955 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.7925 | 97.6137 | 100.0000 | 42.2217 | 2618 | 64 | 2637 | 0 | 0 | ||
| hfeng-pmm3 | INDEL | * | map_l100_m2_e0 | * | 98.6017 | 98.2670 | 98.9388 | 83.3913 | 3629 | 64 | 3636 | 39 | 9 | 23.0769 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.6271 | 96.4286 | 98.8558 | 65.7524 | 1728 | 64 | 1728 | 20 | 18 | 90.0000 | |
| raldana-dualsentieon | INDEL | D1_5 | HG002complexvar | hetalt | 97.5400 | 95.2663 | 99.9249 | 72.3364 | 1288 | 64 | 1331 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | SNP | * | map_l125_m2_e0 | homalt | 99.7723 | 99.6317 | 99.9134 | 65.2834 | 17311 | 64 | 17311 | 15 | 11 | 73.3333 | |
| raldana-dualsentieon | SNP | * | map_l125_m2_e1 | homalt | 99.7744 | 99.6350 | 99.9142 | 65.3032 | 17468 | 64 | 17468 | 15 | 11 | 73.3333 | |
| rpoplin-dv42 | INDEL | * | map_l100_m2_e0 | het | 97.6728 | 97.2258 | 98.1239 | 84.2550 | 2243 | 64 | 2249 | 43 | 19 | 44.1860 | |
| rpoplin-dv42 | SNP | tv | map_l125_m0_e0 | het | 98.3333 | 98.5458 | 98.1217 | 74.3380 | 4337 | 64 | 4336 | 83 | 43 | 51.8072 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 95.4239 | 91.9294 | 99.1946 | 24.7475 | 729 | 64 | 739 | 6 | 6 | 100.0000 | |
| gduggal-snapplat | INDEL | D1_5 | map_l150_m0_e0 | * | 82.2615 | 77.8547 | 87.1972 | 95.7884 | 225 | 64 | 252 | 37 | 10 | 27.0270 | |
| gduggal-snapplat | INDEL | D1_5 | map_l150_m1_e0 | homalt | 83.1300 | 71.9298 | 98.4615 | 91.6560 | 164 | 64 | 192 | 3 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | D1_5 | map_l150_m2_e0 | homalt | 84.2469 | 73.5537 | 98.5782 | 91.9064 | 178 | 64 | 208 | 3 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | D1_5 | map_siren | hetalt | 34.1880 | 23.8095 | 60.6061 | 98.0287 | 20 | 64 | 20 | 13 | 7 | 53.8462 | |
| gduggal-snapplat | INDEL | I1_5 | map_l100_m0_e0 | het | 82.1561 | 80.3681 | 84.0256 | 94.2956 | 262 | 64 | 263 | 50 | 2 | 4.0000 | |
| gduggal-snapplat | INDEL | I1_5 | map_l125_m2_e0 | homalt | 87.6927 | 81.2317 | 95.2703 | 90.2632 | 277 | 64 | 282 | 14 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | I6_15 | map_siren | hetalt | 19.7183 | 11.1111 | 87.5000 | 93.7008 | 8 | 64 | 7 | 1 | 0 | 0.0000 | |