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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
77851-77900 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | * | map_l125_m0_e0 | het | 66.8718 | 63.0324 | 71.2092 | 93.2956 | 370 | 217 | 371 | 150 | 76 | 50.6667 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 83.3458 | 88.4259 | 78.8177 | 87.4581 | 1146 | 150 | 1120 | 301 | 76 | 25.2492 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 89.9308 | 89.1078 | 90.7692 | 60.4401 | 769 | 94 | 767 | 78 | 76 | 97.4359 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 80.9161 | 72.4451 | 91.6304 | 55.0342 | 957 | 364 | 843 | 77 | 76 | 98.7013 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 83.1128 | 95.5215 | 73.5573 | 89.2251 | 1685 | 79 | 1708 | 614 | 76 | 12.3779 | |
| gduggal-bwafb | SNP | * | map_l125_m0_e0 | * | 98.4673 | 98.4266 | 98.5079 | 76.7395 | 19080 | 305 | 19080 | 289 | 76 | 26.2976 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.2808 | 98.8889 | 99.6759 | 57.1851 | 27946 | 314 | 27984 | 91 | 76 | 83.5165 | |
| hfeng-pmm3 | SNP | * | * | * | 99.9548 | 99.9339 | 99.9756 | 18.3516 | 3052601 | 2018 | 3052460 | 744 | 76 | 10.2151 | |
| jli-custom | INDEL | * | * | hetalt | 96.4996 | 93.5214 | 99.6737 | 57.4952 | 23602 | 1635 | 23825 | 78 | 76 | 97.4359 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 94.0384 | 95.2632 | 92.8447 | 81.0891 | 1267 | 63 | 1064 | 82 | 76 | 92.6829 | |
| raldana-dualsentieon | INDEL | I16_PLUS | * | homalt | 97.4343 | 99.7438 | 95.2294 | 67.8023 | 1557 | 4 | 1557 | 78 | 76 | 97.4359 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 90.2936 | 98.1609 | 83.5938 | 71.7906 | 427 | 8 | 428 | 84 | 76 | 90.4762 | |
| ghariani-varprowl | SNP | tv | map_l100_m0_e0 | het | 96.3501 | 99.0446 | 93.7983 | 79.0409 | 7153 | 69 | 7154 | 473 | 76 | 16.0677 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 41.1620 | 27.4615 | 82.1429 | 68.1214 | 410 | 1083 | 414 | 90 | 76 | 84.4444 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 96.8834 | 96.9671 | 96.7998 | 38.7932 | 4476 | 140 | 4507 | 149 | 76 | 51.0067 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 88.0992 | 92.7022 | 83.9316 | 81.2018 | 470 | 37 | 491 | 94 | 76 | 80.8511 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.0189 | 97.0540 | 87.4804 | 71.5621 | 593 | 18 | 559 | 80 | 76 | 95.0000 | |
| bgallagher-sentieon | SNP | ti | * | het | 99.9232 | 99.9613 | 99.8851 | 18.4052 | 1281395 | 496 | 1281341 | 1474 | 76 | 5.1560 | |
| bgallagher-sentieon | INDEL | D16_PLUS | * | het | 97.5876 | 99.3036 | 95.9298 | 78.0298 | 3137 | 22 | 2899 | 123 | 76 | 61.7886 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.0827 | 98.9005 | 93.4211 | 85.4634 | 1799 | 20 | 1562 | 110 | 76 | 69.0909 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.0827 | 98.9005 | 93.4211 | 85.4634 | 1799 | 20 | 1562 | 110 | 76 | 69.0909 | |
| bgallagher-sentieon | INDEL | D1_5 | HG002complexvar | * | 99.6177 | 99.4956 | 99.7400 | 58.4446 | 32550 | 165 | 32605 | 85 | 76 | 89.4118 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.1082 | 92.7162 | 93.5035 | 64.4487 | 1222 | 96 | 1209 | 84 | 76 | 90.4762 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 16.9764 | 10.8209 | 39.3750 | 52.0958 | 58 | 478 | 63 | 97 | 77 | 79.3814 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 20.5715 | 13.2114 | 46.4481 | 71.1356 | 65 | 427 | 85 | 98 | 77 | 78.5714 | |
| anovak-vg | INDEL | D1_5 | map_l125_m1_e0 | * | 83.2162 | 85.2022 | 81.3206 | 87.0514 | 927 | 161 | 936 | 215 | 77 | 35.8140 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.6491 | 95.3947 | 95.9048 | 73.2348 | 2030 | 98 | 2014 | 86 | 77 | 89.5349 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 93.6669 | 99.5017 | 88.4786 | 52.4912 | 599 | 3 | 599 | 78 | 77 | 98.7179 | |
| asubramanian-gatk | INDEL | D6_15 | HG002complexvar | * | 97.5846 | 96.7748 | 98.4081 | 58.8477 | 5131 | 171 | 5131 | 83 | 77 | 92.7711 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.0207 | 95.3171 | 98.7864 | 34.4210 | 6493 | 319 | 6512 | 80 | 77 | 96.2500 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 71.6605 | 91.8919 | 58.7302 | 73.5664 | 136 | 12 | 111 | 78 | 77 | 98.7179 | |
| bgallagher-sentieon | SNP | * | map_siren | het | 99.4455 | 99.6483 | 99.2436 | 58.2943 | 90671 | 320 | 90657 | 691 | 77 | 11.1433 | |
| gduggal-bwafb | SNP | ti | map_l125_m1_e0 | het | 98.5889 | 98.6861 | 98.4920 | 74.2606 | 18026 | 240 | 18026 | 276 | 77 | 27.8986 | |
| gduggal-bwaplat | INDEL | D1_5 | HG002compoundhet | het | 66.9499 | 56.3657 | 82.4278 | 83.5498 | 974 | 754 | 971 | 207 | 77 | 37.1981 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 50.8522 | 34.3937 | 97.5171 | 49.4033 | 2811 | 5362 | 3142 | 80 | 77 | 96.2500 | |
| gduggal-bwavard | INDEL | * | map_l125_m2_e1 | * | 91.5391 | 94.9663 | 88.3507 | 90.2029 | 2113 | 112 | 2116 | 279 | 77 | 27.5986 | |
| gduggal-bwaplat | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 86.1055 | 77.1255 | 97.4522 | 79.8031 | 7475 | 2217 | 7497 | 196 | 77 | 39.2857 | |
| gduggal-bwaplat | SNP | tv | HG002complexvar | homalt | 97.7875 | 95.7534 | 99.9100 | 24.5806 | 91072 | 4039 | 90999 | 82 | 77 | 93.9024 | |
| jpowers-varprowl | INDEL | I16_PLUS | HG002compoundhet | homalt | 7.1429 | 100.0000 | 3.7037 | 66.6667 | 3 | 0 | 3 | 78 | 77 | 98.7179 | |
| jpowers-varprowl | SNP | tv | map_l100_m0_e0 | het | 95.8224 | 96.2337 | 95.4146 | 78.9693 | 6950 | 272 | 6950 | 334 | 77 | 23.0539 | |
| jpowers-varprowl | INDEL | * | map_l125_m1_e0 | * | 93.0277 | 91.5045 | 94.6026 | 87.5701 | 1928 | 179 | 1928 | 110 | 77 | 70.0000 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 89.1082 | 85.6054 | 92.9098 | 41.8941 | 1011 | 170 | 1009 | 77 | 77 | 100.0000 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 91.5006 | 95.9083 | 87.4802 | 71.8304 | 586 | 25 | 552 | 79 | 77 | 97.4684 | |
| jmaeng-gatk | SNP | ti | HG002complexvar | * | 99.5813 | 99.1995 | 99.9661 | 17.9457 | 504366 | 4070 | 504306 | 171 | 77 | 45.0292 | |
| dgrover-gatk | SNP | * | map_siren | het | 99.5699 | 99.6197 | 99.5201 | 59.7603 | 90645 | 346 | 90631 | 437 | 77 | 17.6201 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.6964 | 95.4417 | 95.9524 | 73.2314 | 2031 | 97 | 2015 | 85 | 77 | 90.5882 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 91.5170 | 91.6918 | 91.3428 | 68.3622 | 607 | 55 | 1034 | 98 | 77 | 78.5714 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 96.9297 | 97.2667 | 96.5950 | 72.0063 | 2918 | 82 | 2922 | 103 | 77 | 74.7573 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 70.5915 | 71.0059 | 70.1818 | 64.6075 | 120 | 49 | 193 | 82 | 77 | 93.9024 | |
| ndellapenna-hhga | INDEL | I6_15 | HG002compoundhet | het | 71.9355 | 85.0962 | 62.3003 | 78.5616 | 177 | 31 | 195 | 118 | 77 | 65.2542 | |