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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
13001-13050 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | D16_PLUS | HG002complexvar | het | 76.6298 | 73.5321 | 80.0000 | 57.0120 | 814 | 293 | 488 | 122 | 28 | 22.9508 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 91.0457 | 84.6445 | 98.4943 | 38.8914 | 2679 | 486 | 2682 | 41 | 28 | 68.2927 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 87.7042 | 78.9949 | 98.5719 | 61.4567 | 2971 | 790 | 2968 | 43 | 28 | 65.1163 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 87.7042 | 78.9949 | 98.5719 | 61.4567 | 2971 | 790 | 2968 | 43 | 28 | 65.1163 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 80.9033 | 83.4146 | 78.5388 | 83.2569 | 171 | 34 | 172 | 47 | 28 | 59.5745 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 85.6249 | 79.9127 | 92.2166 | 76.3031 | 549 | 138 | 545 | 46 | 28 | 60.8696 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 80.9033 | 83.4146 | 78.5388 | 83.2569 | 171 | 34 | 172 | 47 | 28 | 59.5745 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 88.5339 | 85.2853 | 92.0398 | 83.8251 | 568 | 98 | 555 | 48 | 27 | 56.2500 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 88.5339 | 85.2853 | 92.0398 | 83.8251 | 568 | 98 | 555 | 48 | 27 | 56.2500 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002complexvar | * | 97.6446 | 97.6263 | 97.6630 | 66.8096 | 1604 | 39 | 1588 | 38 | 27 | 71.0526 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.7426 | 96.1442 | 99.3950 | 25.7739 | 4588 | 184 | 4600 | 28 | 27 | 96.4286 | |
| egarrison-hhga | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2155 | 98.8292 | 99.6047 | 53.9964 | 17642 | 209 | 17640 | 70 | 27 | 38.5714 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 88.1005 | 80.0000 | 98.0263 | 81.2243 | 428 | 107 | 1341 | 27 | 27 | 100.0000 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 72.1154 | 94.9392 | 0 | 0 | 75 | 29 | 27 | 93.1034 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 79.4104 | 79.0850 | 79.7386 | 67.5159 | 121 | 32 | 122 | 31 | 27 | 87.0968 | |
| ckim-isaac | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2969 | 92.1490 | 96.5473 | 61.2007 | 2993 | 255 | 3020 | 108 | 27 | 25.0000 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 97.9052 | 96.1507 | 99.7250 | 58.1999 | 10491 | 420 | 10518 | 29 | 27 | 93.1034 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 90.7836 | 84.1298 | 98.5804 | 37.3201 | 2359 | 445 | 2361 | 34 | 27 | 79.4118 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 71.5265 | 61.2613 | 85.9244 | 78.5005 | 408 | 258 | 409 | 67 | 27 | 40.2985 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 71.5265 | 61.2613 | 85.9244 | 78.5005 | 408 | 258 | 409 | 67 | 27 | 40.2985 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.4580 | 95.5784 | 99.4130 | 24.4663 | 4561 | 211 | 4573 | 27 | 27 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.1514 | 90.4452 | 98.1743 | 66.8941 | 1666 | 176 | 1667 | 31 | 27 | 87.0968 | |
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4494 | 99.3637 | 99.5353 | 61.3550 | 55277 | 354 | 55266 | 258 | 27 | 10.4651 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.4203 | 98.9214 | 95.9641 | 68.3987 | 642 | 7 | 642 | 27 | 27 | 100.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.6923 | 100.0000 | 91.7404 | 70.4446 | 311 | 0 | 311 | 28 | 27 | 96.4286 | |
| dgrover-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.6743 | 99.8742 | 99.4753 | 60.5238 | 55561 | 70 | 55550 | 293 | 27 | 9.2150 | |
| dgrover-gatk | SNP | tv | map_l125_m1_e0 | * | 99.2231 | 99.2882 | 99.1581 | 73.2603 | 15902 | 114 | 15900 | 135 | 27 | 20.0000 | |
| dgrover-gatk | SNP | tv | map_l125_m2_e0 | * | 99.2454 | 99.3086 | 99.1822 | 74.7468 | 16375 | 114 | 16373 | 135 | 27 | 20.0000 | |
| dgrover-gatk | SNP | tv | map_l125_m2_e1 | * | 99.2530 | 99.3156 | 99.1905 | 74.7864 | 16543 | 114 | 16541 | 135 | 27 | 20.0000 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.2951 | 97.8471 | 98.7472 | 84.7253 | 3545 | 78 | 3547 | 45 | 27 | 60.0000 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 19.5122 | 17.3913 | 22.2222 | 55.5556 | 8 | 38 | 8 | 28 | 27 | 96.4286 | |
| gduggal-bwavard | INDEL | D1_5 | * | homalt | 95.1427 | 90.8106 | 99.9088 | 44.5205 | 44430 | 4496 | 43826 | 40 | 27 | 67.5000 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 26.6884 | 15.5852 | 92.8021 | 65.3298 | 257 | 1392 | 361 | 28 | 27 | 96.4286 | |
| eyeh-varpipe | INDEL | D1_5 | map_l100_m2_e1 | homalt | 97.3013 | 98.5484 | 96.0854 | 85.4680 | 611 | 9 | 810 | 33 | 27 | 81.8182 | |
| eyeh-varpipe | INDEL | I1_5 | map_l100_m1_e0 | het | 97.0283 | 97.4260 | 96.6338 | 80.2465 | 757 | 20 | 1177 | 41 | 27 | 65.8537 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 82.7273 | 89.2157 | 77.1186 | 54.2636 | 91 | 11 | 91 | 27 | 27 | 100.0000 | |
| gduggal-bwafb | INDEL | D1_5 | HG002compoundhet | hetalt | 93.3119 | 88.0482 | 99.2450 | 76.1026 | 8995 | 1221 | 3549 | 27 | 27 | 100.0000 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 94.3814 | 92.1127 | 96.7647 | 63.8170 | 981 | 84 | 987 | 33 | 27 | 81.8182 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 85.8733 | 81.0734 | 91.2773 | 61.1380 | 287 | 67 | 293 | 28 | 27 | 96.4286 | |
| eyeh-varpipe | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.4962 | 98.9130 | 94.1946 | 61.4016 | 1729 | 19 | 1655 | 102 | 27 | 26.4706 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 78.4383 | 93.0670 | 67.7838 | 87.7240 | 792 | 59 | 627 | 298 | 27 | 9.0604 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 89.0761 | 81.4952 | 98.2120 | 71.9556 | 1537 | 349 | 1538 | 28 | 27 | 96.4286 | |
| gduggal-bwafb | INDEL | * | map_siren | homalt | 98.3408 | 98.1921 | 98.4900 | 81.3372 | 2607 | 48 | 2609 | 40 | 27 | 67.5000 | |
| gduggal-bwaplat | INDEL | D6_15 | HG002complexvar | hetalt | 82.3891 | 72.0632 | 96.1691 | 62.5248 | 730 | 283 | 728 | 29 | 27 | 93.1034 | |
| gduggal-bwavard | SNP | ti | map_l250_m2_e0 | * | 91.4486 | 97.4840 | 86.1170 | 92.1941 | 4882 | 126 | 4857 | 783 | 27 | 3.4483 | |
| gduggal-bwaplat | INDEL | I1_5 | HG002complexvar | hetalt | 79.1588 | 66.5701 | 97.6190 | 80.6928 | 1149 | 577 | 1148 | 28 | 27 | 96.4286 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 83.2726 | 71.7728 | 99.1604 | 47.4357 | 3425 | 1347 | 3425 | 29 | 27 | 93.1034 | |
| gduggal-bwaplat | SNP | * | map_l150_m2_e0 | het | 74.3081 | 59.3950 | 99.2206 | 92.2348 | 11958 | 8175 | 11966 | 94 | 27 | 28.7234 | |
| gduggal-bwaplat | SNP | * | map_l150_m2_e1 | het | 74.4402 | 59.5688 | 99.2072 | 92.2354 | 12130 | 8233 | 12138 | 97 | 27 | 27.8351 | |
| ltrigg-rtg2 | INDEL | D1_5 | HG002compoundhet | het | 97.0089 | 97.1644 | 96.8539 | 67.7653 | 1679 | 49 | 1724 | 56 | 27 | 48.2143 | |