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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
59501-59550 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.9369 | 89.2961 | 96.8873 | 47.7240 | 2461 | 295 | 2459 | 79 | 77 | 97.4684 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.1736 | 98.3607 | 100.0000 | 47.7208 | 120 | 2 | 367 | 0 | 0 | ||
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 91.0808 | 99.3135 | 84.1085 | 47.7204 | 434 | 3 | 434 | 82 | 82 | 100.0000 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 89.9539 | 95.3891 | 85.1048 | 47.7198 | 4241 | 205 | 11210 | 1962 | 925 | 47.1458 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 84.1219 | 73.6301 | 98.1006 | 47.7187 | 645 | 231 | 1911 | 37 | 37 | 100.0000 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.7839 | 96.9412 | 98.6414 | 47.7167 | 19966 | 630 | 19967 | 275 | 271 | 98.5455 | |
| ltrigg-rtg2 | SNP | tv | map_siren | het | 99.1276 | 98.6962 | 99.5628 | 47.7162 | 28236 | 373 | 28241 | 124 | 4 | 3.2258 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.8288 | 94.8353 | 98.9080 | 47.7162 | 1267 | 69 | 1268 | 14 | 7 | 50.0000 | |
| hfeng-pmm1 | SNP | ti | * | hetalt | 99.5708 | 99.6564 | 99.4854 | 47.7130 | 580 | 2 | 580 | 3 | 3 | 100.0000 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 94.6023 | 95.2631 | 93.9507 | 47.7088 | 9070 | 451 | 9070 | 584 | 265 | 45.3767 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 86.0733 | 85.0400 | 87.1320 | 47.7048 | 27206 | 4786 | 27139 | 4008 | 3953 | 98.6277 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 53.6664 | 37.9233 | 91.7582 | 47.7011 | 168 | 275 | 167 | 15 | 13 | 86.6667 | |
| gduggal-bwaplat | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 91.9813 | 85.4583 | 99.5823 | 47.6985 | 3338 | 568 | 3338 | 14 | 1 | 7.1429 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 71.3186 | 75.9474 | 67.2215 | 47.6957 | 9018 | 2856 | 12237 | 5967 | 4608 | 77.2247 | |
| mlin-fermikit | INDEL | D16_PLUS | HG002compoundhet | het | 55.6184 | 84.9383 | 41.3462 | 47.6949 | 344 | 61 | 258 | 366 | 363 | 99.1803 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 96.5816 | 99.2511 | 94.0520 | 47.6931 | 2783 | 21 | 2783 | 176 | 175 | 99.4318 | |
| anovak-vg | INDEL | * | tech_badpromoters | homalt | 76.1124 | 75.7576 | 76.4706 | 47.6923 | 25 | 8 | 26 | 8 | 7 | 87.5000 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.9071 | 100.0000 | 99.8145 | 47.6826 | 2152 | 0 | 2152 | 4 | 4 | 100.0000 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.2867 | 99.0043 | 99.5708 | 47.6796 | 696 | 7 | 696 | 3 | 2 | 66.6667 | |
| jli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.3548 | 99.1736 | 99.5367 | 47.6794 | 10321 | 86 | 10312 | 48 | 43 | 89.5833 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.4012 | 99.2823 | 99.5204 | 47.6788 | 415 | 3 | 415 | 2 | 1 | 50.0000 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 93.2862 | 87.4172 | 100.0000 | 47.6744 | 132 | 19 | 135 | 0 | 0 | ||
| qzeng-custom | INDEL | D6_15 | * | homalt | 94.3599 | 96.6962 | 92.1338 | 47.6739 | 6117 | 209 | 6114 | 522 | 246 | 47.1264 | |
| gduggal-snapfb | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.3876 | 99.6809 | 99.0961 | 47.6724 | 6248 | 20 | 6249 | 57 | 11 | 19.2982 | |
| asubramanian-gatk | SNP | * | * | hetalt | 94.8157 | 94.4891 | 95.1445 | 47.6709 | 823 | 48 | 823 | 42 | 2 | 4.7619 | |
| jpowers-varprowl | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 70.1373 | 58.7236 | 87.0583 | 47.6620 | 6082 | 4275 | 6061 | 901 | 793 | 88.0133 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 99.0555 | 98.1287 | 100.0000 | 47.6606 | 839 | 16 | 839 | 0 | 0 | ||
| eyeh-varpipe | SNP | * | HG002compoundhet | homalt | 97.1233 | 99.4992 | 94.8583 | 47.6589 | 10728 | 54 | 3616 | 196 | 81 | 41.3265 | |
| jlack-gatk | INDEL | I1_5 | func_cds | * | 97.5741 | 100.0000 | 95.2632 | 47.6584 | 180 | 0 | 181 | 9 | 0 | 0.0000 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 71.1558 | 89.0067 | 59.2690 | 47.6573 | 7473 | 923 | 18665 | 12827 | 11064 | 86.2556 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 71.4286 | 88.8889 | 59.7015 | 47.6562 | 40 | 5 | 40 | 27 | 26 | 96.2963 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.7636 | 100.0000 | 99.5283 | 47.6543 | 211 | 0 | 211 | 1 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 87.9792 | 78.9116 | 99.4012 | 47.6489 | 1276 | 341 | 166 | 1 | 1 | 100.0000 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 95.2915 | 97.2540 | 93.4066 | 47.6410 | 425 | 12 | 425 | 30 | 30 | 100.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 87.8990 | 80.2937 | 97.0958 | 47.6367 | 1039 | 255 | 1237 | 37 | 31 | 83.7838 | |
| jmaeng-gatk | SNP | * | tech_badpromoters | * | 98.0769 | 97.4522 | 98.7097 | 47.6351 | 153 | 4 | 153 | 2 | 2 | 100.0000 | |
| qzeng-custom | SNP | ti | map_siren | homalt | 93.0187 | 87.2719 | 99.5758 | 47.6263 | 33090 | 4826 | 32626 | 139 | 121 | 87.0504 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.6957 | 98.3216 | 99.0726 | 47.6211 | 10896 | 186 | 10896 | 102 | 98 | 96.0784 | |
| eyeh-varpipe | INDEL | D16_PLUS | func_cds | * | 69.5652 | 66.6667 | 72.7273 | 47.6190 | 8 | 4 | 8 | 3 | 3 | 100.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 92.7536 | 88.8889 | 96.9697 | 47.6190 | 32 | 4 | 32 | 1 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | tech_badpromoters | het | 95.2381 | 100.0000 | 90.9091 | 47.6190 | 10 | 0 | 10 | 1 | 1 | 100.0000 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 85.7143 | 75.0000 | 100.0000 | 47.6190 | 9 | 3 | 11 | 0 | 0 | ||
| gduggal-bwafb | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 79.2391 | 67.4470 | 96.0280 | 47.6132 | 605 | 292 | 411 | 17 | 16 | 94.1176 | |
| eyeh-varpipe | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 96.6612 | 97.3341 | 95.9975 | 47.6081 | 1643 | 45 | 1535 | 64 | 22 | 34.3750 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.2840 | 98.5782 | 100.0000 | 47.6071 | 208 | 3 | 208 | 0 | 0 | ||
| jpowers-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 74.2102 | 70.4505 | 78.3938 | 47.6036 | 8366 | 3509 | 8356 | 2303 | 2257 | 98.0026 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 68.5075 | 66.4183 | 70.7325 | 47.6018 | 13192 | 6670 | 15431 | 6385 | 4862 | 76.1472 | |
| jpowers-varprowl | INDEL | I6_15 | * | * | 57.4140 | 50.4492 | 66.6100 | 47.5997 | 12523 | 12300 | 12542 | 6287 | 6247 | 99.3638 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.1109 | 98.8558 | 86.2275 | 47.5941 | 432 | 5 | 432 | 69 | 69 | 100.0000 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 54.3121 | 49.8996 | 59.5807 | 47.5940 | 21624 | 21711 | 28700 | 19470 | 15099 | 77.5501 | |