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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
72901-72950 / 86044 show all | |||||||||||||||
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4006 | 99.5116 | 99.2899 | 63.6333 | 35246 | 173 | 35235 | 252 | 21 | 8.3333 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.1945 | 95.5607 | 98.8851 | 56.8401 | 3724 | 173 | 3725 | 42 | 35 | 83.3333 | |
| gduggal-snapvard | SNP | ti | map_l150_m0_e0 | homalt | 96.4550 | 93.7342 | 99.3385 | 76.5596 | 2588 | 173 | 2553 | 17 | 13 | 76.4706 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 1.1429 | 0.0000 | 0.0000 | 2 | 173 | 0 | 0 | 0 | ||
| ghariani-varprowl | SNP | tv | map_l150_m1_e0 | * | 96.9968 | 98.4146 | 95.6193 | 80.2097 | 10739 | 173 | 10739 | 492 | 89 | 18.0894 | |
| gduggal-snapplat | INDEL | I1_5 | map_l100_m2_e1 | het | 80.9197 | 78.6420 | 83.3333 | 93.5255 | 637 | 173 | 640 | 128 | 3 | 2.3438 | |
| gduggal-snapplat | INDEL | I1_5 | map_l125_m1_e0 | * | 84.1534 | 79.1566 | 89.8236 | 93.4173 | 657 | 173 | 662 | 75 | 4 | 5.3333 | |
| gduggal-snapplat | INDEL | I6_15 | HG002compoundhet | het | 14.0448 | 16.8269 | 12.0521 | 71.7051 | 35 | 173 | 37 | 270 | 38 | 14.0741 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.0553 | 90.6080 | 97.7752 | 66.9888 | 1669 | 173 | 1670 | 38 | 32 | 84.2105 | |
| astatham-gatk | SNP | ti | map_siren | homalt | 99.7489 | 99.5437 | 99.9550 | 48.8366 | 37743 | 173 | 37737 | 17 | 16 | 94.1176 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 26.7404 | 22.0721 | 33.9130 | 42.0655 | 49 | 173 | 78 | 152 | 131 | 86.1842 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 28.5438 | 64.6939 | 18.3115 | 55.1706 | 317 | 173 | 308 | 1374 | 1358 | 98.8355 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.8028 | 97.6785 | 97.9275 | 46.3889 | 7279 | 173 | 7182 | 152 | 45 | 29.6053 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.1153 | 94.1966 | 98.1139 | 51.3592 | 2808 | 173 | 2809 | 54 | 50 | 92.5926 | |
| 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 | |
| jlack-gatk | INDEL | D16_PLUS | HG002compoundhet | hetalt | 95.0565 | 90.9751 | 99.5213 | 25.2782 | 1754 | 174 | 1871 | 9 | 9 | 100.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 98.1326 | 96.3537 | 99.9783 | 25.7249 | 4598 | 174 | 4610 | 1 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | D1_5 | segdup | * | 87.1437 | 84.2248 | 90.2721 | 96.4637 | 929 | 174 | 1095 | 118 | 18 | 15.2542 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 27.5097 | 21.6216 | 37.8049 | 73.8854 | 48 | 174 | 62 | 102 | 48 | 47.0588 | |
| gduggal-snapvard | SNP | ti | segdup | homalt | 98.6062 | 97.6815 | 99.5484 | 88.2591 | 7331 | 174 | 7275 | 33 | 32 | 96.9697 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.8269 | 98.7352 | 98.9188 | 69.0820 | 13583 | 174 | 13540 | 148 | 116 | 78.3784 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.8269 | 98.7352 | 98.9188 | 69.0820 | 13583 | 174 | 13540 | 148 | 116 | 78.3784 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.2162 | 95.0172 | 99.5194 | 52.2792 | 3318 | 174 | 3313 | 16 | 11 | 68.7500 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 0.5714 | 0.0000 | 0.0000 | 1 | 174 | 0 | 0 | 0 | ||
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.1054 | 98.7352 | 99.4784 | 63.8767 | 13583 | 174 | 13541 | 71 | 56 | 78.8732 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.1054 | 98.7352 | 99.4784 | 63.8767 | 13583 | 174 | 13541 | 71 | 56 | 78.8732 | |
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 41.3700 | 79.5535 | 27.9532 | 77.8018 | 677 | 174 | 717 | 1848 | 48 | 2.5974 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.1384 | 90.5537 | 98.0186 | 60.1764 | 1668 | 174 | 1682 | 34 | 29 | 85.2941 | |
| cchapple-custom | INDEL | D16_PLUS | HG002compoundhet | hetalt | 0.0000 | 90.9751 | 0.0000 | 0.0000 | 1754 | 174 | 0 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 94.0865 | 90.1750 | 98.3527 | 42.9913 | 1597 | 174 | 1612 | 27 | 24 | 88.8889 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 79.2712 | 87.6596 | 72.3480 | 57.0624 | 1236 | 174 | 1214 | 464 | 433 | 93.3190 | |
| qzeng-custom | SNP | tv | HG002compoundhet | * | 98.0856 | 98.0500 | 98.1212 | 53.9878 | 8749 | 174 | 9244 | 177 | 64 | 36.1582 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.8283 | 92.7831 | 96.9658 | 59.2331 | 2237 | 174 | 2237 | 70 | 66 | 94.2857 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 82.2286 | 71.0963 | 97.4943 | 44.8492 | 428 | 174 | 428 | 11 | 10 | 90.9091 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 83.6943 | 72.8549 | 98.3229 | 36.6534 | 467 | 174 | 469 | 8 | 6 | 75.0000 | |
| gduggal-bwafb | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.3797 | 99.1386 | 99.6220 | 59.2352 | 20025 | 174 | 20030 | 76 | 54 | 71.0526 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 74.2459 | 71.4286 | 77.2947 | 60.6089 | 435 | 174 | 320 | 94 | 92 | 97.8723 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 49.1296 | 32.8185 | 97.6744 | 58.8517 | 85 | 174 | 84 | 2 | 2 | 100.0000 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 0.5714 | 0.0000 | 0.0000 | 1 | 174 | 0 | 0 | 0 | ||
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 84.6329 | 76.2619 | 95.0680 | 66.4957 | 559 | 174 | 559 | 29 | 29 | 100.0000 | |
| astatham-gatk | INDEL | * | map_l100_m1_e0 | * | 96.5907 | 95.1478 | 98.0780 | 85.9214 | 3412 | 174 | 3419 | 67 | 17 | 25.3731 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.0999 | 94.4231 | 99.9328 | 43.7027 | 2946 | 174 | 2975 | 2 | 2 | 100.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.6470 | 95.4271 | 99.9726 | 29.9483 | 3631 | 174 | 3655 | 1 | 1 | 100.0000 | |
| anovak-vg | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 0.0000 | 44.0895 | 0.0000 | 0.0000 | 138 | 175 | 0 | 0 | 0 | ||
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 68.3076 | 76.1255 | 61.9459 | 62.5658 | 558 | 175 | 573 | 352 | 267 | 75.8523 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 60.9623 | 54.4271 | 69.2810 | 72.5314 | 209 | 175 | 212 | 94 | 51 | 54.2553 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.6340 | 97.1321 | 98.1411 | 72.4105 | 5927 | 175 | 5913 | 112 | 49 | 43.7500 | |
| ndellapenna-hhga | SNP | tv | map_l150_m2_e1 | het | 98.5776 | 97.6184 | 99.5559 | 73.8732 | 7173 | 175 | 7173 | 32 | 13 | 40.6250 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 69.0769 | 53.9474 | 96.0000 | 65.2241 | 205 | 175 | 216 | 9 | 8 | 88.8889 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 91.9346 | 96.5800 | 87.7156 | 44.0577 | 4942 | 175 | 4934 | 691 | 677 | 97.9740 | |