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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16251-16300 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 96.2389 | 96.7975 | 95.6867 | 83.0087 | 937 | 31 | 843 | 38 | 30 | 78.9474 | |
| jli-custom | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4256 | 99.8900 | 98.9654 | 59.3515 | 3634 | 4 | 3635 | 38 | 37 | 97.3684 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 94.2099 | 94.9264 | 93.5043 | 70.1531 | 580 | 31 | 547 | 38 | 36 | 94.7368 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 88.2022 | 97.5155 | 80.5128 | 34.1216 | 157 | 4 | 157 | 38 | 38 | 100.0000 | |
| jli-custom | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.8328 | 92.0195 | 97.8236 | 63.3039 | 1695 | 147 | 1708 | 38 | 31 | 81.5789 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.2132 | 98.0073 | 98.4200 | 74.3056 | 2410 | 49 | 2367 | 38 | 26 | 68.4211 | |
| jli-custom | INDEL | I6_15 | HG002compoundhet | het | 86.7430 | 93.7500 | 80.7107 | 83.6785 | 195 | 13 | 159 | 38 | 30 | 78.9474 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.0900 | 94.8591 | 99.4283 | 33.0075 | 6532 | 354 | 6609 | 38 | 38 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.1659 | 93.1102 | 99.4290 | 31.4906 | 6622 | 490 | 6617 | 38 | 38 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.3258 | 97.0402 | 99.6459 | 43.8344 | 10754 | 328 | 10693 | 38 | 34 | 89.4737 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.0103 | 94.5783 | 99.5706 | 64.1494 | 8792 | 504 | 8811 | 38 | 38 | 100.0000 | |
| jmaeng-gatk | INDEL | D1_5 | map_l125_m0_e0 | het | 94.0671 | 98.5507 | 89.9736 | 92.9238 | 340 | 5 | 341 | 38 | 1 | 2.6316 | |
| ltrigg-rtg1 | SNP | tv | map_l125_m2_e1 | het | 98.7185 | 97.8205 | 99.6332 | 61.5213 | 10323 | 230 | 10322 | 38 | 5 | 13.1579 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 87.9863 | 79.9619 | 97.8009 | 49.2660 | 1680 | 421 | 1690 | 38 | 36 | 94.7368 | |
| ltrigg-rtg2 | INDEL | * | map_l100_m2_e1 | * | 97.6390 | 96.3525 | 98.9603 | 79.8456 | 3619 | 137 | 3617 | 38 | 6 | 15.7895 | |
| gduggal-snapfb | SNP | * | map_l150_m0_e0 | homalt | 95.7170 | 92.6388 | 99.0068 | 86.9094 | 3788 | 301 | 3788 | 38 | 12 | 31.5789 | |
| ghariani-varprowl | INDEL | I1_5 | map_l150_m2_e0 | het | 93.0663 | 97.7346 | 88.8235 | 94.2157 | 302 | 7 | 302 | 38 | 9 | 23.6842 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 74.0111 | 93.5484 | 61.2245 | 84.4444 | 58 | 4 | 60 | 38 | 37 | 97.3684 | |
| ghariani-varprowl | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | het | 71.3785 | 86.3636 | 60.8247 | 96.1886 | 57 | 9 | 59 | 38 | 3 | 7.8947 | |
| ghariani-varprowl | SNP | tv | map_l125_m1_e0 | homalt | 98.8683 | 98.3959 | 99.3453 | 69.2128 | 5766 | 94 | 5766 | 38 | 24 | 63.1579 | |
| ghariani-varprowl | SNP | tv | map_l125_m2_e0 | homalt | 98.8811 | 98.4045 | 99.3623 | 71.6697 | 5921 | 96 | 5921 | 38 | 24 | 63.1579 | |
| ghariani-varprowl | SNP | tv | map_l125_m2_e1 | homalt | 98.8833 | 98.4030 | 99.3682 | 71.6795 | 5977 | 97 | 5977 | 38 | 24 | 63.1579 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 57.4446 | 41.4634 | 93.4708 | 72.4562 | 561 | 792 | 544 | 38 | 36 | 94.7368 | |
| ghariani-varprowl | INDEL | * | func_cds | het | 90.6725 | 97.6636 | 84.6154 | 54.4280 | 209 | 5 | 209 | 38 | 29 | 76.3158 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 68.4170 | 67.7419 | 69.1057 | 99.9232 | 84 | 40 | 85 | 38 | 22 | 57.8947 | |
| ghariani-varprowl | INDEL | D1_5 | map_l250_m2_e0 | het | 84.7826 | 96.6942 | 75.4839 | 96.9295 | 117 | 4 | 117 | 38 | 3 | 7.8947 | |
| ghariani-varprowl | INDEL | D1_5 | map_l250_m2_e1 | het | 84.8921 | 96.7213 | 75.6410 | 96.9838 | 118 | 4 | 118 | 38 | 3 | 7.8947 | |
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 1.1095 | 0.5618 | 44.1176 | 64.0212 | 1 | 177 | 30 | 38 | 22 | 57.8947 | |
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 1.8131 | 0.9259 | 43.2836 | 64.1711 | 1 | 107 | 29 | 38 | 22 | 57.8947 | |
| gduggal-snapvard | SNP | ti | lowcmp_SimpleRepeat_diTR_51to200 | het | 11.7647 | 30.0000 | 7.3171 | 96.1754 | 3 | 7 | 3 | 38 | 0 | 0.0000 | |
| gduggal-snapvard | SNP | ti | map_l100_m1_e0 | homalt | 97.9288 | 96.1470 | 99.7778 | 60.0714 | 17268 | 692 | 17067 | 38 | 31 | 81.5789 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 79.0248 | 67.8719 | 94.5637 | 68.1984 | 657 | 311 | 661 | 38 | 8 | 21.0526 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 20.2653 | 12.1269 | 61.6162 | 73.8786 | 65 | 471 | 61 | 38 | 4 | 10.5263 | |
| eyeh-varpipe | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 0.0000 | 0.0000 | 38.7097 | 93.8796 | 0 | 0 | 24 | 38 | 25 | 65.7895 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 24.4790 | 14.1603 | 90.2314 | 68.8301 | 258 | 1564 | 351 | 38 | 31 | 81.5789 | |
| eyeh-varpipe | INDEL | D6_15 | map_l100_m2_e1 | homalt | 74.3512 | 83.5821 | 66.9565 | 84.9279 | 56 | 11 | 77 | 38 | 35 | 92.1053 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 92.3366 | 91.0042 | 93.7086 | 71.1832 | 435 | 43 | 566 | 38 | 38 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | func_cds | * | 99.4984 | 99.2747 | 99.7231 | 31.1374 | 13687 | 100 | 13687 | 38 | 4 | 10.5263 | |
| gduggal-bwaplat | SNP | ti | func_cds | het | 99.4112 | 99.2709 | 99.5519 | 36.3268 | 8442 | 62 | 8442 | 38 | 4 | 10.5263 | |
| gduggal-bwavard | INDEL | * | func_cds | * | 92.3991 | 93.2584 | 91.5556 | 46.3647 | 415 | 30 | 412 | 38 | 24 | 63.1579 | |
| gduggal-bwavard | INDEL | * | func_cds | het | 91.1447 | 98.5981 | 84.7390 | 55.3763 | 211 | 3 | 211 | 38 | 24 | 63.1579 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 59.7005 | 42.6942 | 99.2246 | 54.0503 | 4903 | 6581 | 4863 | 38 | 33 | 86.8421 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 71.9701 | 57.8195 | 95.2912 | 87.3887 | 769 | 561 | 769 | 38 | 33 | 86.8421 | |
| gduggal-bwafb | INDEL | I1_5 | HG002complexvar | hetalt | 89.3217 | 83.8355 | 95.5763 | 80.3162 | 1447 | 279 | 821 | 38 | 37 | 97.3684 | |
| gduggal-bwavard | INDEL | I1_5 | map_l100_m0_e0 | het | 92.9247 | 96.9325 | 89.2351 | 90.6242 | 316 | 10 | 315 | 38 | 12 | 31.5789 | |
| gduggal-bwavard | INDEL | I1_5 | map_l150_m2_e1 | het | 93.4841 | 98.4227 | 89.0173 | 93.4950 | 312 | 5 | 308 | 38 | 14 | 36.8421 | |
| gduggal-bwavard | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | * | 67.8971 | 71.2871 | 64.8148 | 95.6696 | 72 | 29 | 70 | 38 | 8 | 21.0526 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 73.3083 | 94.2029 | 60.0000 | 83.8710 | 65 | 4 | 57 | 38 | 9 | 23.6842 | |
| eyeh-varpipe | SNP | ti | map_l250_m0_e0 | * | 98.2427 | 99.2701 | 97.2364 | 94.1737 | 1360 | 10 | 1337 | 38 | 1 | 2.6316 | |
| eyeh-varpipe | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.0184 | 98.5852 | 97.4582 | 45.8333 | 1742 | 25 | 1457 | 38 | 11 | 28.9474 | |