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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
77801-77850 / 86044 show all | |||||||||||||||
| gduggal-snapplat | INDEL | I1_5 | segdup | * | 78.0848 | 75.0708 | 81.3508 | 96.7377 | 795 | 264 | 807 | 185 | 6 | 3.2432 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 96.1382 | 99.7890 | 92.7451 | 61.9630 | 2365 | 5 | 2365 | 185 | 184 | 99.4595 | |
| ndellapenna-hhga | SNP | * | HG002complexvar | het | 99.7473 | 99.5353 | 99.9601 | 18.3091 | 463334 | 2163 | 463353 | 185 | 79 | 42.7027 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.5341 | 99.1135 | 96.0043 | 33.9044 | 559 | 5 | 4445 | 185 | 173 | 93.5135 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5725 | 99.1852 | 92.2138 | 66.1587 | 2191 | 18 | 2191 | 185 | 182 | 98.3784 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.0520 | 99.8745 | 98.2429 | 45.7715 | 10344 | 13 | 10344 | 185 | 181 | 97.8378 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.0004 | 98.7335 | 95.3271 | 68.1496 | 3820 | 49 | 3774 | 185 | 180 | 97.2973 | |
| ltrigg-rtg2 | INDEL | * | * | homalt | 99.5524 | 99.2554 | 99.8512 | 52.3128 | 124239 | 932 | 124115 | 185 | 162 | 87.5676 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 40.3286 | 26.9258 | 80.2982 | 58.7796 | 755 | 2049 | 754 | 185 | 171 | 92.4324 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 90.4630 | 88.1350 | 92.9173 | 49.6530 | 2429 | 327 | 2427 | 185 | 180 | 97.2973 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.1732 | 94.9348 | 95.4128 | 68.8499 | 3861 | 206 | 3848 | 185 | 153 | 82.7027 | |
| eyeh-varpipe | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 95.6922 | 99.9080 | 91.8178 | 68.6059 | 2172 | 2 | 2076 | 185 | 3 | 1.6216 | |
| gduggal-bwafb | SNP | tv | map_l150_m2_e0 | * | 98.5004 | 98.6262 | 98.3749 | 78.4095 | 11199 | 156 | 11199 | 185 | 38 | 20.5405 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 85.3804 | 75.9374 | 97.5054 | 58.4142 | 7230 | 2291 | 7231 | 185 | 160 | 86.4865 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 67.7108 | 95.5224 | 52.4422 | 85.5605 | 192 | 9 | 204 | 185 | 99 | 53.5135 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m2_e1 | het | 92.4908 | 98.8170 | 86.9258 | 89.0233 | 1253 | 15 | 1230 | 185 | 49 | 26.4865 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 65.0184 | 70.8333 | 60.0858 | 84.4511 | 272 | 112 | 280 | 186 | 100 | 53.7634 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.6955 | 99.6275 | 95.8371 | 67.9253 | 4279 | 16 | 4282 | 186 | 9 | 4.8387 | |
| gduggal-bwafb | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 96.6316 | 99.0933 | 94.2892 | 74.2061 | 3060 | 28 | 3071 | 186 | 41 | 22.0430 | |
| gduggal-bwafb | SNP | tv | map_l150_m2_e1 | * | 98.5152 | 98.6437 | 98.3871 | 78.4497 | 11346 | 156 | 11346 | 186 | 38 | 20.4301 | |
| anovak-vg | INDEL | I1_5 | map_l100_m2_e0 | het | 48.1704 | 38.4615 | 64.4359 | 89.9093 | 305 | 488 | 337 | 186 | 31 | 16.6667 | |
| anovak-vg | INDEL | I1_5 | map_l100_m2_e1 | het | 47.7657 | 37.9012 | 64.5714 | 90.0794 | 307 | 503 | 339 | 186 | 31 | 16.6667 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.8931 | 97.7585 | 98.0280 | 45.2710 | 9246 | 212 | 9246 | 186 | 181 | 97.3118 | |
| qzeng-custom | INDEL | D16_PLUS | map_siren | het | 51.9122 | 88.4615 | 36.7347 | 86.9217 | 69 | 9 | 108 | 186 | 12 | 6.4516 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 84.8521 | 85.8447 | 83.8821 | 72.0175 | 752 | 124 | 968 | 186 | 175 | 94.0860 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 82.5967 | 81.0065 | 84.2506 | 51.7959 | 998 | 234 | 995 | 186 | 167 | 89.7849 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 89.7993 | 95.4044 | 84.8163 | 74.1070 | 1038 | 50 | 1039 | 186 | 169 | 90.8602 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.4167 | 97.7259 | 97.1096 | 71.4786 | 6274 | 146 | 6249 | 186 | 32 | 17.2043 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.4167 | 97.7259 | 97.1096 | 71.4786 | 6274 | 146 | 6249 | 186 | 32 | 17.2043 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 18.3861 | 14.4397 | 25.3012 | 64.2755 | 67 | 397 | 63 | 186 | 4 | 2.1505 | |
| ciseli-custom | INDEL | D6_15 | map_siren | * | 62.3762 | 61.8861 | 62.8743 | 84.5131 | 315 | 194 | 315 | 186 | 97 | 52.1505 | |
| ckim-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.5094 | 99.6893 | 99.3302 | 65.3964 | 27592 | 86 | 27582 | 186 | 18 | 9.6774 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 91.8999 | 88.1227 | 96.0154 | 66.8254 | 4511 | 608 | 4482 | 186 | 78 | 41.9355 | |
| ckim-vqsr | SNP | ti | map_l100_m1_e0 | * | 77.5493 | 63.5768 | 99.3932 | 81.5266 | 30473 | 17458 | 30468 | 186 | 13 | 6.9893 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.8527 | 99.9044 | 97.8230 | 55.8586 | 8358 | 8 | 8358 | 186 | 184 | 98.9247 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 76.5556 | 82.5342 | 71.3846 | 62.2751 | 723 | 153 | 464 | 186 | 158 | 84.9462 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 83.4511 | 77.1464 | 90.8779 | 45.5977 | 1860 | 551 | 1853 | 186 | 163 | 87.6344 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 71.2396 | 76.0246 | 67.0213 | 78.1818 | 371 | 117 | 378 | 186 | 179 | 96.2366 | |
| ltrigg-rtg1 | INDEL | * | HG002complexvar | het | 98.9136 | 98.2515 | 99.5847 | 53.0906 | 45404 | 808 | 44604 | 186 | 79 | 42.4731 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9856 | 97.6629 | 98.3105 | 52.2428 | 10823 | 259 | 10823 | 186 | 181 | 97.3118 | |
| jli-custom | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.9793 | 99.8507 | 96.1768 | 39.7598 | 4682 | 7 | 4679 | 186 | 1 | 0.5376 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.3197 | 98.8079 | 95.8756 | 69.0152 | 4393 | 53 | 4347 | 187 | 182 | 97.3262 | |
| ckim-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5308 | 99.1852 | 92.1362 | 66.1398 | 2191 | 18 | 2191 | 187 | 184 | 98.3957 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.8013 | 97.5893 | 98.0142 | 45.3295 | 9230 | 228 | 9230 | 187 | 180 | 96.2567 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.0217 | 94.2549 | 97.8560 | 49.0716 | 3675 | 224 | 8535 | 187 | 123 | 65.7754 | |
| ltrigg-rtg2 | SNP | ti | map_siren | het | 99.2569 | 98.8202 | 99.6976 | 45.2238 | 61645 | 736 | 61646 | 187 | 11 | 5.8824 | |
| qzeng-custom | SNP | ti | HG002compoundhet | het | 98.0838 | 97.7380 | 98.4320 | 42.6883 | 9290 | 215 | 11739 | 187 | 45 | 24.0642 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m2_e1 | * | 92.7581 | 94.9974 | 90.6219 | 86.9648 | 1842 | 97 | 1807 | 187 | 51 | 27.2727 | |
| gduggal-snapfb | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 50.6602 | 37.5000 | 78.0516 | 49.9118 | 1434 | 2390 | 665 | 187 | 113 | 60.4278 | |
| anovak-vg | SNP | tv | segdup | * | 97.7325 | 97.6676 | 97.7974 | 93.3295 | 8333 | 199 | 8303 | 187 | 80 | 42.7807 | |