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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
69351-69400 / 86044 show all | |||||||||||||||
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 37.5614 | 34.6667 | 40.9836 | 65.1429 | 26 | 49 | 25 | 36 | 31 | 86.1111 | |
| eyeh-varpipe | INDEL | D6_15 | map_l100_m2_e0 | homalt | 74.5239 | 83.0769 | 67.5676 | 84.9389 | 54 | 11 | 75 | 36 | 33 | 91.6667 | |
| gduggal-bwafb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.5924 | 99.6528 | 97.5543 | 73.9929 | 1435 | 5 | 1436 | 36 | 3 | 8.3333 | |
| gduggal-bwaplat | INDEL | D16_PLUS | HG002complexvar | * | 76.5914 | 63.4206 | 96.6667 | 72.4490 | 1042 | 601 | 1044 | 36 | 23 | 63.8889 | |
| eyeh-varpipe | INDEL | I6_15 | map_siren | * | 77.9593 | 69.5082 | 88.7500 | 73.3555 | 212 | 93 | 284 | 36 | 33 | 91.6667 | |
| gduggal-bwafb | INDEL | D16_PLUS | HG002complexvar | het | 83.6409 | 73.8031 | 96.5049 | 50.3136 | 817 | 290 | 994 | 36 | 33 | 91.6667 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 89.7351 | 86.0317 | 93.7716 | 60.6535 | 542 | 88 | 542 | 36 | 19 | 52.7778 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 91.2250 | 84.5061 | 99.1045 | 23.0475 | 3927 | 720 | 3984 | 36 | 30 | 83.3333 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.7315 | 91.7481 | 97.9155 | 67.3720 | 1690 | 152 | 1691 | 36 | 30 | 83.3333 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.2214 | 97.1584 | 99.3078 | 64.5805 | 5163 | 151 | 5165 | 36 | 29 | 80.5556 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.5490 | 95.8600 | 99.2985 | 63.8541 | 5094 | 220 | 5096 | 36 | 30 | 83.3333 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 93.8354 | 92.2330 | 95.4944 | 66.5970 | 760 | 64 | 763 | 36 | 33 | 91.6667 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 90.3594 | 93.8224 | 87.1429 | 56.0440 | 243 | 16 | 244 | 36 | 30 | 83.3333 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 84.8057 | 94.4882 | 76.9231 | 49.6774 | 120 | 7 | 120 | 36 | 30 | 83.3333 | |
| egarrison-hhga | INDEL | D6_15 | map_siren | * | 91.4556 | 90.1768 | 92.7711 | 83.2942 | 459 | 50 | 462 | 36 | 21 | 58.3333 | |
| ckim-isaac | SNP | ti | HG002complexvar | homalt | 95.8992 | 92.1386 | 99.9798 | 16.1839 | 178255 | 15209 | 178286 | 36 | 29 | 80.5556 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 96.7084 | 94.4652 | 99.0608 | 42.7483 | 3789 | 222 | 3797 | 36 | 12 | 33.3333 | |
| ckim-isaac | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | het | 66.2722 | 72.7273 | 60.8696 | 89.6513 | 48 | 18 | 56 | 36 | 4 | 11.1111 | |
| ckim-vqsr | INDEL | * | segdup | * | 98.6516 | 98.7089 | 98.5943 | 95.8809 | 2523 | 33 | 2525 | 36 | 10 | 27.7778 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002complexvar | * | 97.6423 | 97.5046 | 97.7805 | 66.9855 | 1602 | 41 | 1586 | 36 | 28 | 77.7778 | |
| egarrison-hhga | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3197 | 98.9592 | 99.6829 | 37.2866 | 11314 | 119 | 11317 | 36 | 17 | 47.2222 | |
| egarrison-hhga | SNP | * | segdup | homalt | 99.7815 | 99.8976 | 99.6657 | 89.1087 | 10732 | 11 | 10732 | 36 | 36 | 100.0000 | |
| egarrison-hhga | SNP | ti | map_l100_m0_e0 | * | 99.3678 | 98.9068 | 99.8331 | 66.9886 | 21533 | 238 | 21534 | 36 | 20 | 55.5556 | |
| egarrison-hhga | SNP | tv | map_l100_m1_e0 | het | 99.3126 | 98.8649 | 99.7644 | 63.7472 | 15242 | 175 | 15242 | 36 | 13 | 36.1111 | |
| egarrison-hhga | SNP | tv | map_l125_m2_e0 | * | 99.4065 | 99.0357 | 99.7800 | 70.1050 | 16330 | 159 | 16330 | 36 | 17 | 47.2222 | |
| egarrison-hhga | SNP | tv | map_l125_m2_e1 | * | 99.4064 | 99.0334 | 99.7822 | 70.1626 | 16496 | 161 | 16496 | 36 | 17 | 47.2222 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.0000 | 75.8389 | 94.4299 | 0 | 0 | 113 | 36 | 34 | 94.4444 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 77.0103 | 95.8580 | 64.3564 | 80.8712 | 162 | 7 | 65 | 36 | 36 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.3774 | 93.8671 | 99.0257 | 55.4228 | 3658 | 239 | 3659 | 36 | 29 | 80.5556 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.7656 | 98.4611 | 99.0719 | 67.7717 | 3839 | 60 | 3843 | 36 | 22 | 61.1111 | |
| jlack-gatk | INDEL | I1_5 | map_l150_m2_e0 | het | 93.2231 | 97.4110 | 89.3805 | 93.8420 | 301 | 8 | 303 | 36 | 2 | 5.5556 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 76.6255 | 94.6746 | 64.3564 | 81.0507 | 160 | 9 | 65 | 36 | 36 | 100.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.4720 | 97.5389 | 99.4231 | 74.9870 | 6262 | 158 | 6204 | 36 | 21 | 58.3333 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.4720 | 97.5389 | 99.4231 | 74.9870 | 6262 | 158 | 6204 | 36 | 21 | 58.3333 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.4390 | 99.1515 | 95.7845 | 70.5720 | 818 | 7 | 818 | 36 | 34 | 94.4444 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.4390 | 99.1515 | 95.7845 | 70.5720 | 818 | 7 | 818 | 36 | 34 | 94.4444 | |
| hfeng-pmm2 | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.4758 | 99.1531 | 99.8007 | 37.5709 | 18029 | 154 | 18026 | 36 | 2 | 5.5556 | |
| jlack-gatk | INDEL | D1_5 | map_l250_m1_e0 | * | 89.6000 | 98.2456 | 82.3529 | 96.3309 | 168 | 3 | 168 | 36 | 1 | 2.7778 | |
| jlack-gatk | INDEL | D1_5 | map_l250_m1_e0 | het | 85.1562 | 98.1982 | 75.1724 | 96.7963 | 109 | 2 | 109 | 36 | 1 | 2.7778 | |
| jlack-gatk | INDEL | D1_5 | map_l250_m2_e0 | * | 90.2743 | 98.3696 | 83.4101 | 96.5457 | 181 | 3 | 181 | 36 | 1 | 2.7778 | |
| jlack-gatk | INDEL | D1_5 | map_l250_m2_e0 | het | 86.2319 | 98.3471 | 76.7742 | 96.9560 | 119 | 2 | 119 | 36 | 1 | 2.7778 | |
| jlack-gatk | INDEL | D1_5 | map_l250_m2_e1 | * | 90.3226 | 98.3784 | 83.4862 | 96.6186 | 182 | 3 | 182 | 36 | 1 | 2.7778 | |
| jlack-gatk | INDEL | D1_5 | map_l250_m2_e1 | het | 86.3309 | 98.3607 | 76.9231 | 97.0115 | 120 | 2 | 120 | 36 | 1 | 2.7778 | |
| jlack-gatk | INDEL | D6_15 | map_siren | het | 92.5170 | 97.1429 | 88.3117 | 88.1992 | 272 | 8 | 272 | 36 | 3 | 8.3333 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.8949 | 94.4670 | 99.4508 | 25.3587 | 6505 | 381 | 6519 | 36 | 36 | 100.0000 | |
| ckim-dragen | INDEL | D1_5 | map_l125_m1_e0 | * | 97.0194 | 97.3346 | 96.7063 | 87.6399 | 1059 | 29 | 1057 | 36 | 5 | 13.8889 | |
| ckim-dragen | INDEL | D6_15 | HG002complexvar | hetalt | 93.7506 | 91.2142 | 96.4321 | 47.8822 | 924 | 89 | 973 | 36 | 36 | 100.0000 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.4252 | 93.5104 | 99.5276 | 29.6399 | 7536 | 523 | 7584 | 36 | 36 | 100.0000 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.4252 | 93.5104 | 99.5276 | 29.6399 | 7536 | 523 | 7584 | 36 | 36 | 100.0000 | |
| ckim-dragen | INDEL | I1_5 | HG002complexvar | het | 99.6858 | 99.5712 | 99.8007 | 57.6433 | 18111 | 78 | 18030 | 36 | 22 | 61.1111 | |