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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
21201-21250 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 87.3886 | 77.9606 | 99.4105 | 51.5253 | 5734 | 1621 | 5734 | 34 | 6 | 17.6471 | |
| dgrover-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.4457 | 99.4809 | 99.4105 | 79.4316 | 4216 | 22 | 4216 | 25 | 7 | 28.0000 | |
| ckim-isaac | INDEL | * | map_siren | homalt | 82.0615 | 69.8682 | 99.4105 | 72.7551 | 1855 | 800 | 1855 | 11 | 7 | 63.6364 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.9335 | 98.4611 | 99.4104 | 64.3027 | 3839 | 60 | 3878 | 23 | 7 | 30.4348 | |
| mlin-fermikit | SNP | tv | * | * | 98.7665 | 98.1308 | 99.4104 | 19.3147 | 951572 | 18126 | 951506 | 5643 | 4116 | 72.9399 | |
| anovak-vg | SNP | ti | map_l250_m1_e0 | homalt | 84.7951 | 73.9266 | 99.4103 | 87.1481 | 1188 | 419 | 1180 | 7 | 5 | 71.4286 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.7600 | 86.9438 | 99.4102 | 29.9035 | 1485 | 223 | 1517 | 9 | 8 | 88.8889 | |
| asubramanian-gatk | INDEL | D1_5 | map_l125_m2_e0 | homalt | 95.8748 | 92.5824 | 99.4100 | 87.0065 | 337 | 27 | 337 | 2 | 1 | 50.0000 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l125_m2_e0 | homalt | 99.1176 | 98.8270 | 99.4100 | 83.4553 | 337 | 4 | 337 | 2 | 1 | 50.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l125_m2_e1 | homalt | 99.1211 | 98.8338 | 99.4100 | 80.8041 | 339 | 4 | 337 | 2 | 0 | 0.0000 | |
| ltrigg-rtg1 | SNP | tv | map_l150_m0_e0 | het | 97.1210 | 94.9349 | 99.4100 | 64.2688 | 2699 | 144 | 2696 | 16 | 3 | 18.7500 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 98.3942 | 97.3988 | 99.4100 | 77.7413 | 337 | 9 | 337 | 2 | 1 | 50.0000 | |
| jli-custom | INDEL | * | segdup | * | 99.1762 | 98.9437 | 99.4099 | 94.0244 | 2529 | 27 | 2527 | 15 | 7 | 46.6667 | |
| ckim-dragen | INDEL | D1_5 | * | homalt | 99.6542 | 99.8998 | 99.4098 | 63.4062 | 48877 | 49 | 48847 | 290 | 286 | 98.6207 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 99.2628 | 99.1167 | 99.4094 | 87.9803 | 2693 | 24 | 2693 | 16 | 14 | 87.5000 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 96.6320 | 94.0056 | 99.4094 | 36.1609 | 2023 | 129 | 2020 | 12 | 9 | 75.0000 | |
| ckim-dragen | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.8829 | 98.3619 | 99.4094 | 51.8057 | 2642 | 44 | 2693 | 16 | 3 | 18.7500 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.3040 | 97.2229 | 99.4094 | 71.0102 | 32313 | 923 | 38374 | 228 | 113 | 49.5614 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.3720 | 99.3348 | 99.4092 | 74.3463 | 1344 | 9 | 1346 | 8 | 3 | 37.5000 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 99.2442 | 99.0799 | 99.4092 | 87.9842 | 2692 | 25 | 2692 | 16 | 14 | 87.5000 | |
| cchapple-custom | INDEL | * | segdup | het | 99.0552 | 98.7040 | 99.4090 | 95.0259 | 1447 | 19 | 1682 | 10 | 3 | 30.0000 | |
| gduggal-bwaplat | SNP | * | map_l125_m2_e0 | * | 75.1671 | 60.4306 | 99.4087 | 87.7400 | 28235 | 18488 | 28242 | 168 | 47 | 27.9762 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.2758 | 93.3345 | 99.4086 | 38.9346 | 5503 | 393 | 6051 | 36 | 34 | 94.4444 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.2758 | 93.3345 | 99.4086 | 38.9346 | 5503 | 393 | 6051 | 36 | 34 | 94.4444 | |
| ltrigg-rtg2 | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4910 | 99.5737 | 99.4084 | 59.3516 | 27560 | 118 | 27559 | 164 | 14 | 8.5366 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 95.9057 | 92.6415 | 99.4083 | 55.1724 | 491 | 39 | 504 | 3 | 3 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | HG002complexvar | het | 91.1805 | 84.2105 | 99.4083 | 47.5155 | 560 | 105 | 504 | 3 | 2 | 66.6667 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 96.8300 | 94.3820 | 99.4083 | 77.2237 | 168 | 10 | 168 | 1 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.6479 | 90.3226 | 99.4083 | 69.9288 | 168 | 18 | 168 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.5337 | 97.6744 | 99.4083 | 80.0236 | 168 | 4 | 168 | 1 | 1 | 100.0000 | |
| ckim-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.5862 | 99.7647 | 99.4083 | 59.0715 | 17809 | 42 | 17808 | 106 | 7 | 6.6038 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.6479 | 90.3226 | 99.4083 | 67.9924 | 168 | 18 | 168 | 1 | 1 | 100.0000 | |
| qzeng-custom | SNP | ti | segdup | homalt | 99.3042 | 99.2005 | 99.4081 | 87.0359 | 7445 | 60 | 7390 | 44 | 39 | 88.6364 | |
| gduggal-snapvard | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.5046 | 97.6173 | 99.4081 | 39.4232 | 3892 | 95 | 3863 | 23 | 9 | 39.1304 | |
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.0360 | 92.8854 | 99.4078 | 87.3434 | 1175 | 90 | 1175 | 7 | 6 | 85.7143 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.1965 | 97.0144 | 99.4078 | 64.7466 | 15597 | 480 | 15611 | 93 | 72 | 77.4194 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.1965 | 97.0144 | 99.4078 | 64.7466 | 15597 | 480 | 15611 | 93 | 72 | 77.4194 | |
| gduggal-bwaplat | SNP | * | map_l100_m2_e1 | * | 82.9577 | 71.1789 | 99.4078 | 82.2985 | 53197 | 21540 | 53209 | 317 | 87 | 27.4448 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4891 | 99.5708 | 99.4077 | 75.9619 | 21805 | 94 | 21817 | 130 | 120 | 92.3077 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.6357 | 90.3010 | 99.4076 | 53.2928 | 810 | 87 | 839 | 5 | 5 | 100.0000 | |
| gduggal-bwaplat | SNP | * | map_l100_m2_e0 | * | 82.8217 | 70.9791 | 99.4075 | 82.3292 | 52499 | 21465 | 52511 | 313 | 86 | 27.4760 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4251 | 99.4428 | 99.4073 | 78.7466 | 6068 | 34 | 6038 | 36 | 13 | 36.1111 | |
| cchapple-custom | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.6239 | 99.8416 | 99.4072 | 41.3357 | 10715 | 17 | 10732 | 64 | 7 | 10.9375 | |
| cchapple-custom | INDEL | I1_5 | map_l100_m1_e0 | homalt | 98.7338 | 98.0695 | 99.4071 | 79.0129 | 508 | 10 | 503 | 3 | 2 | 66.6667 | |
| mlin-fermikit | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.0436 | 96.7173 | 99.4069 | 53.0396 | 17265 | 586 | 17262 | 103 | 9 | 8.7379 | |
| gduggal-bwaplat | SNP | * | map_l125_m2_e1 | * | 75.3654 | 60.6881 | 99.4067 | 87.7186 | 28646 | 18556 | 28653 | 171 | 47 | 27.4854 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.5051 | 99.6037 | 99.4067 | 88.7962 | 1508 | 6 | 1508 | 9 | 9 | 100.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.3535 | 95.3835 | 99.4066 | 24.9710 | 3843 | 186 | 3853 | 23 | 21 | 91.3043 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.3885 | 93.5484 | 99.4065 | 59.1515 | 319 | 22 | 335 | 2 | 2 | 100.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.0966 | 96.8208 | 99.4065 | 69.4192 | 335 | 11 | 335 | 2 | 0 | 0.0000 | |