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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
65351-65400 / 86044 show all | |||||||||||||||
| gduggal-snapfb | INDEL | I16_PLUS | HG002compoundhet | het | 0.0000 | 2.1277 | 0.0000 | 0.0000 | 1 | 46 | 0 | 0 | 0 | ||
| gduggal-snapplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 0.0000 | 0.0000 | 0.0000 | 0 | 46 | 0 | 0 | 0 | |||
| gduggal-snapplat | INDEL | D16_PLUS | map_l100_m1_e0 | het | 0.0000 | 0.0000 | 0.0000 | 0 | 46 | 0 | 0 | 0 | |||
| gduggal-snapplat | INDEL | D6_15 | map_l125_m2_e0 | het | 47.0393 | 35.2113 | 70.8333 | 94.8052 | 25 | 46 | 17 | 7 | 1 | 14.2857 | |
| gduggal-snapplat | INDEL | D6_15 | map_l125_m2_e1 | het | 47.0393 | 35.2113 | 70.8333 | 94.8608 | 25 | 46 | 17 | 7 | 1 | 14.2857 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 3.5430 | 9.8039 | 2.1622 | 93.6492 | 5 | 46 | 4 | 181 | 0 | 0.0000 | |
| gduggal-snapfb | SNP | * | map_l250_m0_e0 | homalt | 95.3393 | 92.6868 | 98.1481 | 96.7438 | 583 | 46 | 583 | 11 | 5 | 45.4545 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 20.7663 | 68.9189 | 12.2249 | 46.1133 | 102 | 46 | 100 | 718 | 715 | 99.5822 | |
| ghariani-varprowl | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 97.4281 | 99.0035 | 95.9022 | 49.9948 | 4570 | 46 | 4587 | 196 | 1 | 0.5102 | |
| ghariani-varprowl | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.2300 | 99.5784 | 96.9176 | 63.0014 | 10865 | 46 | 10879 | 346 | 49 | 14.1618 | |
| hfeng-pmm1 | INDEL | * | map_l100_m0_e0 | * | 97.6521 | 97.0569 | 98.2547 | 83.9206 | 1517 | 46 | 1520 | 27 | 6 | 22.2222 | |
| hfeng-pmm1 | INDEL | * | map_l150_m2_e0 | * | 97.6365 | 96.7330 | 98.5570 | 88.7837 | 1362 | 46 | 1366 | 20 | 4 | 20.0000 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 54.2811 | 37.8378 | 96.0000 | 79.1667 | 28 | 46 | 24 | 1 | 1 | 100.0000 | |
| gduggal-snapvard | INDEL | D6_15 | map_siren | het | 75.8046 | 83.5714 | 69.3587 | 81.7036 | 234 | 46 | 292 | 129 | 84 | 65.1163 | |
| gduggal-snapvard | INDEL | I6_15 | map_l100_m2_e0 | * | 60.8455 | 60.3448 | 61.3546 | 79.4431 | 70 | 46 | 154 | 97 | 79 | 81.4433 | |
| gduggal-snapvard | INDEL | I6_15 | map_l100_m2_e1 | * | 60.9208 | 60.3448 | 61.5079 | 79.7590 | 70 | 46 | 155 | 97 | 79 | 81.4433 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 17.6471 | 11.5385 | 37.5000 | 85.1852 | 6 | 46 | 6 | 10 | 7 | 70.0000 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 0.0000 | 0.0000 | 66.6667 | 0 | 46 | 0 | 3 | 2 | 66.6667 | ||
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 95.0122 | 93.7922 | 96.2644 | 75.4150 | 695 | 46 | 670 | 26 | 21 | 80.7692 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.6261 | 95.2133 | 90.1758 | 75.1797 | 915 | 46 | 872 | 95 | 85 | 89.4737 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 93.2622 | 98.0574 | 88.9141 | 86.8298 | 2322 | 46 | 2350 | 293 | 14 | 4.7782 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.5306 | 93.3042 | 97.8659 | 82.3181 | 641 | 46 | 642 | 14 | 11 | 78.5714 | |
| bgallagher-sentieon | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4306 | 99.8701 | 98.9950 | 61.8984 | 35373 | 46 | 35362 | 359 | 20 | 5.5710 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 20.8955 | 13.2075 | 50.0000 | 55.5556 | 7 | 46 | 8 | 8 | 2 | 25.0000 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.9433 | 96.4451 | 99.4887 | 36.9705 | 1248 | 46 | 1362 | 7 | 7 | 100.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.4123 | 91.4179 | 97.6096 | 63.6495 | 490 | 46 | 490 | 12 | 10 | 83.3333 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.3553 | 99.7468 | 97.0021 | 67.1820 | 18120 | 46 | 18120 | 560 | 541 | 96.6071 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.3553 | 99.7468 | 97.0021 | 67.1820 | 18120 | 46 | 18120 | 560 | 541 | 96.6071 | |
| asubramanian-gatk | SNP | tv | HG002compoundhet | hetalt | 95.8824 | 94.5476 | 97.2554 | 25.0447 | 815 | 47 | 815 | 23 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.5180 | 99.5769 | 99.4593 | 62.5780 | 11061 | 47 | 11036 | 60 | 22 | 36.6667 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.9771 | 96.4259 | 97.5347 | 52.3145 | 1268 | 47 | 1266 | 32 | 24 | 75.0000 | |
| bgallagher-sentieon | INDEL | I16_PLUS | * | het | 98.5008 | 98.2708 | 98.7318 | 75.5383 | 2671 | 47 | 2647 | 34 | 10 | 29.4118 | |
| bgallagher-sentieon | SNP | ti | map_l125_m1_e0 | homalt | 99.7370 | 99.5745 | 99.9001 | 63.0037 | 10998 | 47 | 10998 | 11 | 9 | 81.8182 | |
| astatham-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.8706 | 96.2846 | 99.5098 | 88.3340 | 1218 | 47 | 1218 | 6 | 6 | 100.0000 | |
| asubramanian-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 92.7368 | 97.8723 | 88.1133 | 66.0895 | 2162 | 47 | 2209 | 298 | 219 | 73.4899 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 92.3613 | 88.6473 | 96.4000 | 70.3264 | 367 | 47 | 482 | 18 | 17 | 94.4444 | |
| asubramanian-gatk | SNP | * | HG002compoundhet | hetalt | 95.0437 | 94.5476 | 95.5451 | 26.8439 | 815 | 47 | 815 | 38 | 0 | 0.0000 | |
| anovak-vg | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.4369 | 98.7908 | 98.0854 | 58.8485 | 3840 | 47 | 3996 | 78 | 33 | 42.3077 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 92.6984 | 90.4665 | 95.0431 | 49.8920 | 446 | 47 | 441 | 23 | 12 | 52.1739 | |
| anovak-vg | INDEL | D1_5 | map_l250_m2_e0 | * | 72.9497 | 74.4565 | 71.5026 | 96.2008 | 137 | 47 | 138 | 55 | 24 | 43.6364 | |
| anovak-vg | INDEL | D1_5 | map_l250_m2_e1 | * | 72.7100 | 74.5946 | 70.9184 | 96.2235 | 138 | 47 | 139 | 57 | 24 | 42.1053 | |
| anovak-vg | INDEL | I16_PLUS | HG002compoundhet | het | 0.0000 | 0.0000 | 45.8564 | 44.3077 | 0 | 47 | 83 | 98 | 29 | 29.5918 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 77.2602 | 64.3939 | 96.5517 | 88.2749 | 85 | 47 | 84 | 3 | 2 | 66.6667 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 89.8753 | 95.0578 | 85.2286 | 76.3056 | 904 | 47 | 727 | 126 | 44 | 34.9206 | |
| eyeh-varpipe | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.4056 | 99.5621 | 95.3406 | 49.3281 | 10685 | 47 | 10497 | 513 | 52 | 10.1365 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.5178 | 97.0789 | 100.0000 | 47.9893 | 1562 | 47 | 1552 | 0 | 0 | ||
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 96.3560 | 93.3144 | 99.6025 | 30.4588 | 656 | 47 | 1253 | 5 | 4 | 80.0000 | |
| gduggal-bwafb | INDEL | D6_15 | map_l100_m2_e0 | * | 89.1561 | 82.1970 | 97.4026 | 85.7934 | 217 | 47 | 225 | 6 | 3 | 50.0000 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 96.3342 | 95.5238 | 97.1585 | 61.3924 | 1003 | 47 | 889 | 26 | 23 | 88.4615 | |
| gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.0824 | 98.8212 | 99.3451 | 39.8485 | 3940 | 47 | 3944 | 26 | 15 | 57.6923 | |