PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
45751-45800 / 86044 show all | |||||||||||||||
| gduggal-bwavard | INDEL | D6_15 | map_l125_m2_e0 | homalt | 89.2308 | 80.5556 | 100.0000 | 84.6591 | 29 | 7 | 27 | 0 | 0 | ||
| gduggal-bwafb | INDEL | * | * | hetalt | 87.6150 | 80.5643 | 96.0183 | 78.7583 | 20332 | 4905 | 6728 | 279 | 275 | 98.5663 | |
| gduggal-bwafb | INDEL | * | HG002compoundhet | hetalt | 88.3144 | 80.5679 | 97.7090 | 73.4740 | 20287 | 4893 | 6696 | 157 | 155 | 98.7261 | |
| anovak-vg | SNP | * | HG002compoundhet | homalt | 80.7165 | 80.5695 | 80.8640 | 38.2684 | 8687 | 2095 | 7974 | 1887 | 1143 | 60.5723 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 89.0056 | 80.5701 | 99.4139 | 40.3057 | 3081 | 743 | 3223 | 19 | 17 | 89.4737 | |
| gduggal-snapfb | INDEL | I6_15 | segdup | * | 85.8304 | 80.5714 | 91.8239 | 87.1255 | 141 | 34 | 146 | 13 | 13 | 100.0000 | |
| ndellapenna-hhga | INDEL | D16_PLUS | HG002complexvar | * | 84.9902 | 80.5843 | 89.9058 | 63.0348 | 1324 | 319 | 1336 | 150 | 106 | 70.6667 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 88.8394 | 80.5907 | 98.9691 | 22.4000 | 191 | 46 | 192 | 2 | 1 | 50.0000 | |
| ckim-isaac | INDEL | I1_5 | map_siren | * | 88.5873 | 80.5990 | 98.3333 | 78.2801 | 2422 | 583 | 2419 | 41 | 12 | 29.2683 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 89.0334 | 80.6002 | 99.4376 | 31.3443 | 1907 | 459 | 1945 | 11 | 10 | 90.9091 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 89.1544 | 80.6020 | 99.7372 | 41.6858 | 723 | 174 | 759 | 2 | 2 | 100.0000 | |
| mlin-fermikit | SNP | * | map_siren | homalt | 84.4526 | 80.6077 | 88.6825 | 45.6664 | 44460 | 10696 | 44453 | 5673 | 5485 | 96.6861 | |
| anovak-vg | SNP | ti | map_l250_m0_e0 | het | 69.1155 | 80.6210 | 60.4839 | 96.0595 | 753 | 181 | 750 | 490 | 108 | 22.0408 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 86.2084 | 80.6245 | 92.6232 | 55.4837 | 3279 | 788 | 3252 | 259 | 195 | 75.2896 | |
| rpoplin-dv42 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 87.3637 | 80.6250 | 95.3317 | 77.1605 | 387 | 93 | 388 | 19 | 18 | 94.7368 | |
| ckim-isaac | INDEL | * | HG002compoundhet | het | 56.9247 | 80.6302 | 43.9912 | 64.9439 | 3301 | 793 | 2405 | 3062 | 2738 | 89.4187 | |
| anovak-vg | INDEL | * | map_l125_m0_e0 | homalt | 73.9644 | 80.6338 | 68.3140 | 87.4544 | 229 | 55 | 235 | 109 | 101 | 92.6606 | |
| anovak-vg | SNP | tv | map_l250_m2_e0 | * | 73.9754 | 80.6384 | 68.3294 | 91.4956 | 2324 | 558 | 2315 | 1073 | 260 | 24.2311 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 80.6384 | 100.0000 | 5785 | 1389 | 0 | 0 | 0 | ||||
| ckim-isaac | INDEL | D6_15 | HG002complexvar | het | 83.3579 | 80.6410 | 86.2642 | 49.0301 | 2516 | 604 | 1972 | 314 | 100 | 31.8471 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 85.4239 | 80.6452 | 90.8046 | 75.2137 | 50 | 12 | 158 | 16 | 16 | 100.0000 | |
| gduggal-bwafb | INDEL | I6_15 | HG002compoundhet | homalt | 9.4162 | 80.6452 | 5.0000 | 41.3146 | 25 | 6 | 25 | 475 | 473 | 99.5789 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 87.0010 | 80.6452 | 94.4444 | 79.8319 | 50 | 12 | 68 | 4 | 4 | 100.0000 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 68.1961 | 80.6452 | 59.0765 | 60.9919 | 950 | 228 | 934 | 647 | 601 | 92.8903 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 87.3170 | 80.6452 | 95.1923 | 99.9131 | 100 | 24 | 99 | 5 | 0 | 0.0000 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 80.8625 | 80.6452 | 81.0811 | 77.1605 | 50 | 12 | 60 | 14 | 13 | 92.8571 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | map_siren | hetalt | 89.2857 | 80.6452 | 100.0000 | 80.8000 | 25 | 6 | 24 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 88.9077 | 80.6452 | 99.0566 | 99.9183 | 100 | 24 | 105 | 1 | 1 | 100.0000 | |
| gduggal-snapplat | INDEL | D1_5 | map_l125_m2_e0 | * | 85.6819 | 80.6649 | 91.3644 | 92.9665 | 922 | 221 | 1058 | 100 | 21 | 21.0000 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 80.6665 | 100.0000 | 5737 | 1375 | 0 | 0 | 0 | ||||
| gduggal-snapvard | SNP | * | HG002compoundhet | * | 79.9672 | 80.6669 | 79.2796 | 52.8107 | 20829 | 4992 | 20864 | 5453 | 2407 | 44.1408 | |
| mlin-fermikit | INDEL | I6_15 | * | * | 85.1815 | 80.6671 | 90.2311 | 47.3715 | 20024 | 4799 | 20108 | 2177 | 2161 | 99.2650 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 75.6587 | 80.6700 | 71.2335 | 62.4381 | 3034 | 727 | 2974 | 1201 | 1094 | 91.0908 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 75.6587 | 80.6700 | 71.2335 | 62.4381 | 3034 | 727 | 2974 | 1201 | 1094 | 91.0908 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 86.9377 | 80.6789 | 94.2492 | 85.0311 | 309 | 74 | 295 | 18 | 10 | 55.5556 | |
| ckim-gatk | SNP | tv | map_siren | homalt | 89.2983 | 80.6845 | 99.9712 | 58.8566 | 13910 | 3330 | 13907 | 4 | 3 | 75.0000 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 83.2366 | 80.6994 | 85.9386 | 73.3453 | 4131 | 988 | 5091 | 833 | 775 | 93.0372 | |
| ckim-gatk | SNP | ti | map_siren | hetalt | 87.6190 | 80.7018 | 95.8333 | 80.9524 | 46 | 11 | 46 | 2 | 2 | 100.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 89.3204 | 80.7018 | 100.0000 | 99.3925 | 46 | 11 | 46 | 0 | 0 | ||
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 74.5086 | 80.7087 | 69.1932 | 71.0477 | 615 | 147 | 849 | 378 | 216 | 57.1429 | |
| astatham-gatk | SNP | ti | map_l125_m0_e0 | het | 89.1339 | 80.7092 | 99.5223 | 81.9410 | 6669 | 1594 | 6667 | 32 | 13 | 40.6250 | |
| ckim-gatk | SNP | tv | map_l100_m2_e0 | * | 88.3659 | 80.7254 | 97.6039 | 81.5961 | 20208 | 4825 | 20204 | 496 | 17 | 3.4274 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 82.5257 | 80.7309 | 84.4021 | 51.3080 | 486 | 116 | 487 | 90 | 65 | 72.2222 | |
| anovak-vg | SNP | tv | map_l125_m1_e0 | homalt | 88.9946 | 80.7338 | 99.1387 | 66.3699 | 4731 | 1129 | 4719 | 41 | 30 | 73.1707 | |
| jmaeng-gatk | SNP | tv | map_siren | homalt | 89.3303 | 80.7367 | 99.9713 | 58.2484 | 13919 | 3321 | 13916 | 4 | 4 | 100.0000 | |
| ckim-isaac | INDEL | D16_PLUS | * | * | 86.5111 | 80.7488 | 93.1589 | 55.2640 | 5478 | 1306 | 5447 | 400 | 246 | 61.5000 | |
| gduggal-bwaplat | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 89.2731 | 80.7561 | 99.7985 | 45.8371 | 5447 | 1298 | 5447 | 11 | 11 | 100.0000 | |
| anovak-vg | INDEL | I6_15 | * | homalt | 61.4755 | 80.7661 | 49.6232 | 33.6435 | 5039 | 1200 | 5202 | 5281 | 4685 | 88.7143 | |
| asubramanian-gatk | INDEL | D16_PLUS | map_l100_m1_e0 | hetalt | 87.5829 | 80.7692 | 95.6522 | 79.6460 | 21 | 5 | 22 | 1 | 1 | 100.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | map_l100_m2_e0 | hetalt | 87.6588 | 80.7692 | 95.8333 | 80.1653 | 21 | 5 | 23 | 1 | 1 | 100.0000 | |