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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
69901-69950 / 86044 show all | |||||||||||||||
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.5419 | 95.5335 | 99.6365 | 30.2678 | 10609 | 496 | 10690 | 39 | 38 | 97.4359 | |
| anovak-vg | INDEL | * | func_cds | homalt | 87.7119 | 91.5929 | 84.1463 | 33.8710 | 207 | 19 | 207 | 39 | 35 | 89.7436 | |
| anovak-vg | INDEL | I16_PLUS | HG002complexvar | het | 24.3337 | 14.7368 | 69.7674 | 51.5038 | 98 | 567 | 90 | 39 | 9 | 23.0769 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9660 | 98.1027 | 97.8297 | 69.4907 | 1758 | 34 | 1758 | 39 | 30 | 76.9231 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.7103 | 95.9230 | 99.5655 | 64.4709 | 8917 | 379 | 8936 | 39 | 38 | 97.4359 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.0717 | 94.7636 | 99.4951 | 30.0679 | 7637 | 422 | 7685 | 39 | 38 | 97.4359 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.0717 | 94.7636 | 99.4951 | 30.0679 | 7637 | 422 | 7685 | 39 | 38 | 97.4359 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0437 | 98.7072 | 99.3825 | 75.7366 | 6337 | 83 | 6277 | 39 | 26 | 66.6667 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0437 | 98.7072 | 99.3825 | 75.7366 | 6337 | 83 | 6277 | 39 | 26 | 66.6667 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.6303 | 99.8788 | 95.4809 | 71.6678 | 824 | 1 | 824 | 39 | 38 | 97.4359 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.6303 | 99.8788 | 95.4809 | 71.6678 | 824 | 1 | 824 | 39 | 38 | 97.4359 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.9023 | 98.7458 | 99.0593 | 82.5203 | 4094 | 52 | 4107 | 39 | 10 | 25.6410 | |
| bgallagher-sentieon | INDEL | D6_15 | * | hetalt | 96.5632 | 93.7974 | 99.4971 | 32.7057 | 7667 | 507 | 7716 | 39 | 38 | 97.4359 | |
| astatham-gatk | SNP | * | segdup | het | 98.7752 | 97.7998 | 99.7702 | 91.3893 | 16936 | 381 | 16930 | 39 | 2 | 5.1282 | |
| astatham-gatk | SNP | ti | map_l150_m2_e0 | het | 86.0268 | 75.7084 | 99.6015 | 83.8910 | 9752 | 3129 | 9748 | 39 | 19 | 48.7179 | |
| astatham-gatk | SNP | ti | map_l150_m2_e1 | het | 86.0111 | 75.6819 | 99.6055 | 83.9600 | 9850 | 3165 | 9846 | 39 | 19 | 48.7179 | |
| asubramanian-gatk | INDEL | C16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 0.0000 | 0.0000 | 87.6972 | 0 | 0 | 0 | 39 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | C6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 79.0323 | 0 | 0 | 0 | 39 | 0 | 0.0000 | ||
| raldana-dualsentieon | SNP | ti | map_l250_m0_e0 | * | 97.4527 | 97.7372 | 97.1698 | 91.9458 | 1339 | 31 | 1339 | 39 | 1 | 2.5641 | |
| raldana-dualsentieon | SNP | tv | map_l250_m1_e0 | * | 98.0065 | 97.5066 | 98.5115 | 87.3534 | 2581 | 66 | 2581 | 39 | 3 | 7.6923 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7077 | 99.6531 | 99.7624 | 58.0995 | 16372 | 57 | 16373 | 39 | 28 | 71.7949 | |
| raldana-dualsentieon | INDEL | D6_15 | HG002complexvar | * | 96.9018 | 94.6813 | 99.2289 | 57.2443 | 5020 | 282 | 5019 | 39 | 37 | 94.8718 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.2637 | 96.9355 | 99.6289 | 78.1445 | 10470 | 331 | 10470 | 39 | 11 | 28.2051 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.9410 | 92.7025 | 99.4141 | 25.1041 | 6593 | 519 | 6617 | 39 | 38 | 97.4359 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.9098 | 92.6401 | 99.4187 | 25.8018 | 6646 | 528 | 6670 | 39 | 38 | 97.4359 | |
| rpoplin-dv42 | SNP | * | map_l125_m2_e0 | homalt | 99.5066 | 99.2403 | 99.7743 | 69.1861 | 17243 | 132 | 17243 | 39 | 38 | 97.4359 | |
| rpoplin-dv42 | SNP | * | map_l125_m2_e1 | homalt | 99.5110 | 99.2471 | 99.7764 | 69.2363 | 17400 | 132 | 17400 | 39 | 38 | 97.4359 | |
| ckim-isaac | SNP | ti | map_l125_m2_e1 | * | 75.3035 | 60.4665 | 99.7895 | 72.3331 | 18484 | 12085 | 18484 | 39 | 8 | 20.5128 | |
| ckim-vqsr | INDEL | * | map_l125_m0_e0 | * | 96.5169 | 97.3923 | 95.6570 | 93.0361 | 859 | 23 | 859 | 39 | 4 | 10.2564 | |
| eyeh-varpipe | INDEL | * | map_l125_m2_e0 | homalt | 96.9360 | 97.2477 | 96.6263 | 87.0809 | 742 | 21 | 1117 | 39 | 35 | 89.7436 | |
| eyeh-varpipe | INDEL | * | map_l125_m2_e1 | homalt | 96.9786 | 97.2868 | 96.6724 | 87.1688 | 753 | 21 | 1133 | 39 | 35 | 89.7436 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 84.0816 | 96.2647 | 0 | 0 | 206 | 39 | 28 | 71.7949 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 97.2920 | 97.3799 | 97.2043 | 69.4213 | 1338 | 36 | 1356 | 39 | 10 | 25.6410 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 84.2971 | 80.2083 | 88.8252 | 77.8834 | 308 | 76 | 310 | 39 | 36 | 92.3077 | |
| egarrison-hhga | INDEL | D6_15 | HG002compoundhet | hetalt | 65.0591 | 48.4726 | 98.9014 | 28.1522 | 3951 | 4200 | 3511 | 39 | 34 | 87.1795 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 78.6885 | 100.0000 | 64.8649 | 84.3441 | 169 | 0 | 72 | 39 | 38 | 97.4359 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.7887 | 96.0736 | 99.5661 | 64.7766 | 8931 | 365 | 8950 | 39 | 38 | 97.4359 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.1571 | 94.8660 | 99.5615 | 32.7282 | 8814 | 477 | 8855 | 39 | 37 | 94.8718 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.1571 | 94.8660 | 99.5615 | 32.7282 | 8814 | 477 | 8855 | 39 | 37 | 94.8718 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.1156 | 95.4467 | 98.8438 | 53.2567 | 3333 | 159 | 3334 | 39 | 32 | 82.0513 | |
| egarrison-hhga | INDEL | * | map_l100_m0_e0 | * | 97.3109 | 97.1209 | 97.5016 | 98.2621 | 1518 | 45 | 1522 | 39 | 11 | 28.2051 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.1537 | 99.4096 | 96.9291 | 83.2983 | 1347 | 8 | 1231 | 39 | 30 | 76.9231 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 91.4428 | 98.3425 | 85.4478 | 84.5800 | 356 | 6 | 229 | 39 | 37 | 94.8718 | |
| ckim-vqsr | INDEL | D1_5 | HG002compoundhet | hetalt | 96.5656 | 93.7157 | 99.5943 | 58.2787 | 9574 | 642 | 9574 | 39 | 39 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | * | hetalt | 96.8555 | 94.3479 | 99.5000 | 32.9551 | 7712 | 462 | 7761 | 39 | 39 | 100.0000 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.3603 | 99.2881 | 99.4326 | 81.7523 | 6834 | 49 | 6834 | 39 | 15 | 38.4615 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m1_e0 | het | 96.5230 | 96.3606 | 96.6860 | 89.4465 | 1165 | 44 | 1167 | 40 | 4 | 10.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m2_e0 | het | 96.5708 | 96.3376 | 96.8051 | 89.9162 | 1210 | 46 | 1212 | 40 | 4 | 10.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m2_e1 | het | 96.5215 | 96.2145 | 96.8304 | 89.9905 | 1220 | 48 | 1222 | 40 | 4 | 10.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_siren | het | 97.8636 | 97.4967 | 98.2332 | 85.9953 | 2220 | 57 | 2224 | 40 | 2 | 5.0000 | |