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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
71901-71950 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.0673 | 90.9611 | 99.5617 | 70.9107 | 1590 | 158 | 1590 | 7 | 6 | 85.7143 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 92.5771 | 86.4295 | 99.6662 | 81.9053 | 2089 | 328 | 2090 | 7 | 6 | 85.7143 | |
| gduggal-bwaplat | SNP | ti | map_siren | homalt | 87.4388 | 77.6954 | 99.9762 | 56.7476 | 29459 | 8457 | 29428 | 7 | 6 | 85.7143 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 80.6406 | 68.2128 | 98.6056 | 59.6463 | 500 | 233 | 495 | 7 | 6 | 85.7143 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 94.6607 | 91.0166 | 98.6088 | 31.6968 | 6079 | 600 | 5954 | 84 | 72 | 85.7143 | |
| eyeh-varpipe | INDEL | D1_5 | map_l125_m0_e0 | homalt | 97.3470 | 97.9730 | 96.7290 | 90.0047 | 145 | 3 | 207 | 7 | 6 | 85.7143 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 18.7138 | 10.4396 | 90.2235 | 66.4165 | 247 | 2119 | 323 | 35 | 30 | 85.7143 | |
| eyeh-varpipe | INDEL | D6_15 | map_l100_m0_e0 | het | 91.4037 | 93.3333 | 89.5522 | 86.6534 | 56 | 4 | 60 | 7 | 6 | 85.7143 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 95.8166 | 94.3609 | 97.3180 | 80.3612 | 251 | 15 | 254 | 7 | 6 | 85.7143 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 60.4651 | 56.5217 | 65.0000 | 70.1493 | 13 | 10 | 13 | 7 | 6 | 85.7143 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 50.5495 | 37.7049 | 76.6667 | 71.4286 | 23 | 38 | 23 | 7 | 6 | 85.7143 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 97.0511 | 96.3351 | 97.7778 | 77.6754 | 920 | 35 | 924 | 21 | 18 | 85.7143 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 96.7462 | 97.6596 | 95.8498 | 63.4393 | 459 | 11 | 485 | 21 | 18 | 85.7143 | |
| gduggal-bwafb | SNP | * | map_l125_m0_e0 | homalt | 99.3333 | 98.7783 | 99.8945 | 72.5403 | 6630 | 82 | 6630 | 7 | 6 | 85.7143 | |
| gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 86.4865 | 91.4286 | 82.0513 | 92.3228 | 32 | 3 | 32 | 7 | 6 | 85.7143 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 85.2919 | 75.6705 | 97.7165 | 64.9393 | 8690 | 2794 | 8687 | 203 | 174 | 85.7143 | |
| gduggal-bwavard | INDEL | D1_5 | tech_badpromoters | * | 64.5598 | 68.4211 | 61.1111 | 50.0000 | 13 | 6 | 11 | 7 | 6 | 85.7143 | |
| gduggal-bwavard | INDEL | D1_5 | tech_badpromoters | het | 69.5652 | 100.0000 | 53.3333 | 51.6129 | 8 | 0 | 8 | 7 | 6 | 85.7143 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 59.5561 | 42.5651 | 99.1245 | 51.1308 | 1603 | 2163 | 1585 | 14 | 12 | 85.7143 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 55.0595 | 38.1013 | 99.2214 | 43.7774 | 903 | 1467 | 892 | 7 | 6 | 85.7143 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 59.5561 | 42.5651 | 99.1245 | 51.1308 | 1603 | 2163 | 1585 | 14 | 12 | 85.7143 | |
| gduggal-bwafb | INDEL | * | map_l100_m1_e0 | homalt | 98.5277 | 98.2070 | 98.8506 | 84.0137 | 1205 | 22 | 1204 | 14 | 12 | 85.7143 | |
| gduggal-bwafb | INDEL | * | map_l100_m2_e0 | homalt | 98.5676 | 98.2554 | 98.8818 | 84.8792 | 1239 | 22 | 1238 | 14 | 12 | 85.7143 | |
| gduggal-bwafb | INDEL | D16_PLUS | map_siren | het | 83.1234 | 76.9231 | 90.4110 | 81.1370 | 60 | 18 | 66 | 7 | 6 | 85.7143 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 94.4108 | 90.6200 | 98.5326 | 48.7374 | 5072 | 525 | 11281 | 168 | 144 | 85.7143 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 87.4562 | 79.3003 | 97.4820 | 62.2795 | 272 | 71 | 271 | 7 | 6 | 85.7143 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.8164 | 89.8325 | 98.1699 | 67.2797 | 751 | 85 | 751 | 14 | 12 | 85.7143 | |
| jmaeng-gatk | SNP | tv | HG002compoundhet | homalt | 99.4223 | 99.0555 | 99.7918 | 42.9493 | 3356 | 32 | 3355 | 7 | 6 | 85.7143 | |
| jmaeng-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.9011 | 98.5761 | 99.2282 | 89.6010 | 900 | 13 | 900 | 7 | 6 | 85.7143 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 77.3118 | 66.0300 | 93.2432 | 67.5642 | 484 | 249 | 483 | 35 | 30 | 85.7143 | |
| jpowers-varprowl | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 76.1858 | 63.3364 | 95.5758 | 44.5914 | 1363 | 789 | 1361 | 63 | 54 | 85.7143 | |
| jmaeng-gatk | INDEL | I16_PLUS | HG002complexvar | homalt | 98.8800 | 100.0000 | 97.7848 | 70.4949 | 309 | 0 | 309 | 7 | 6 | 85.7143 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 86.7925 | 100.0000 | 76.6667 | 88.6792 | 23 | 0 | 23 | 7 | 6 | 85.7143 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 83.2407 | 74.8148 | 93.8053 | 65.0155 | 101 | 34 | 106 | 7 | 6 | 85.7143 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 90.7360 | 87.1622 | 94.6154 | 66.3212 | 129 | 19 | 123 | 7 | 6 | 85.7143 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0960 | 96.8307 | 99.3948 | 47.7739 | 5744 | 188 | 5748 | 35 | 30 | 85.7143 | |
| jli-custom | SNP | * | HG002compoundhet | homalt | 99.8794 | 99.8887 | 99.8702 | 35.2217 | 10770 | 12 | 10769 | 14 | 12 | 85.7143 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.5329 | 95.5556 | 97.5304 | 68.9206 | 2537 | 118 | 2488 | 63 | 54 | 85.7143 | |
| jpowers-varprowl | INDEL | I1_5 | map_l100_m2_e1 | homalt | 97.4695 | 96.2963 | 98.6717 | 76.3359 | 520 | 20 | 520 | 7 | 6 | 85.7143 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 74.9430 | 62.9630 | 92.5532 | 76.6169 | 85 | 50 | 87 | 7 | 6 | 85.7143 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.6211 | 94.4615 | 98.8818 | 35.5967 | 614 | 36 | 619 | 7 | 6 | 85.7143 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 90.3872 | 86.4865 | 94.6565 | 71.5217 | 128 | 20 | 124 | 7 | 6 | 85.7143 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 85.0894 | 75.5459 | 97.3929 | 69.1734 | 519 | 168 | 523 | 14 | 12 | 85.7143 | |
| ltrigg-rtg1 | INDEL | I6_15 | HG002compoundhet | hetalt | 95.0169 | 90.5822 | 99.9083 | 29.3644 | 7733 | 804 | 7628 | 7 | 6 | 85.7143 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.5354 | 98.1623 | 98.9114 | 65.7432 | 641 | 12 | 636 | 7 | 6 | 85.7143 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.6797 | 97.9695 | 99.4002 | 28.6675 | 1158 | 24 | 1160 | 7 | 6 | 85.7143 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 89.2308 | 100.0000 | 80.5556 | 83.4862 | 22 | 0 | 29 | 7 | 6 | 85.7143 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 91.1519 | 95.1220 | 87.5000 | 86.9767 | 39 | 2 | 49 | 7 | 6 | 85.7143 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 95.8691 | 93.6803 | 98.1627 | 71.5034 | 252 | 17 | 374 | 7 | 6 | 85.7143 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.1124 | 95.2081 | 99.0944 | 24.4379 | 755 | 38 | 766 | 7 | 6 | 85.7143 | |