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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
17501-17550 / 86044 show all | |||||||||||||||
| astatham-gatk | INDEL | * | map_l150_m2_e0 | het | 95.2620 | 94.1501 | 96.4004 | 91.7487 | 853 | 53 | 857 | 32 | 4 | 12.5000 | |
| astatham-gatk | INDEL | * | map_l150_m2_e1 | het | 95.1831 | 93.9394 | 96.4602 | 91.7945 | 868 | 56 | 872 | 32 | 4 | 12.5000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8531 | 99.8195 | 99.8867 | 58.0732 | 28209 | 51 | 28212 | 32 | 20 | 62.5000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 96.7299 | 97.1074 | 96.3554 | 83.0174 | 940 | 28 | 846 | 32 | 22 | 68.7500 | |
| bgallagher-sentieon | INDEL | * | segdup | * | 98.9462 | 99.1393 | 98.7539 | 94.5996 | 2534 | 22 | 2536 | 32 | 11 | 34.3750 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3205 | 99.5404 | 97.1300 | 67.2155 | 1083 | 5 | 1083 | 32 | 26 | 81.2500 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 96.8262 | 99.5074 | 94.2857 | 83.6449 | 606 | 3 | 528 | 32 | 23 | 71.8750 | |
| bgallagher-sentieon | INDEL | D6_15 | HG002compoundhet | hetalt | 96.6337 | 93.8535 | 99.5837 | 23.7576 | 7650 | 501 | 7654 | 32 | 32 | 100.0000 | |
| anovak-vg | INDEL | D1_5 | map_l100_m2_e1 | homalt | 89.8740 | 85.8065 | 94.3463 | 82.6911 | 532 | 88 | 534 | 32 | 29 | 90.6250 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 69.9850 | 66.9291 | 73.3333 | 68.5864 | 85 | 42 | 88 | 32 | 20 | 62.5000 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 11.7647 | 6.8750 | 40.7407 | 67.2727 | 11 | 149 | 22 | 32 | 14 | 43.7500 | |
| astatham-gatk | SNP | * | map_l250_m0_e0 | * | 93.8786 | 89.7892 | 98.3581 | 93.7904 | 1917 | 218 | 1917 | 32 | 8 | 25.0000 | |
| astatham-gatk | SNP | ti | map_l125_m0_e0 | het | 89.1339 | 80.7092 | 99.5223 | 81.9410 | 6669 | 1594 | 6667 | 32 | 13 | 40.6250 | |
| astatham-gatk | SNP | ti | segdup | * | 99.2327 | 98.6385 | 99.8342 | 89.7728 | 19271 | 266 | 19269 | 32 | 6 | 18.7500 | |
| asubramanian-gatk | INDEL | * | map_l250_m1_e0 | het | 83.2020 | 83.1579 | 83.2461 | 97.3234 | 158 | 32 | 159 | 32 | 3 | 9.3750 | |
| asubramanian-gatk | INDEL | * | map_l250_m2_e0 | het | 83.9329 | 83.3333 | 84.5411 | 97.4454 | 175 | 35 | 175 | 32 | 3 | 9.3750 | |
| asubramanian-gatk | INDEL | * | map_l250_m2_e1 | het | 83.7321 | 82.9384 | 84.5411 | 97.5144 | 175 | 36 | 175 | 32 | 3 | 9.3750 | |
| asubramanian-gatk | INDEL | C16_PLUS | HG002complexvar | * | 0.0000 | 0.0000 | 80.4878 | 0 | 0 | 0 | 32 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 0.0000 | 0.0000 | 81.0651 | 0 | 0 | 0 | 32 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | D16_PLUS | * | homalt | 98.2891 | 98.4634 | 98.1154 | 70.9396 | 1666 | 26 | 1666 | 32 | 25 | 78.1250 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.7654 | 98.0785 | 97.4543 | 75.1188 | 1225 | 24 | 1225 | 32 | 25 | 78.1250 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.7654 | 98.0785 | 97.4543 | 75.1188 | 1225 | 24 | 1225 | 32 | 25 | 78.1250 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4789 | 99.8586 | 99.1021 | 72.7252 | 3532 | 5 | 3532 | 32 | 32 | 100.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.9771 | 96.4259 | 97.5347 | 52.3145 | 1268 | 47 | 1266 | 32 | 24 | 75.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | HG002complexvar | homalt | 99.8440 | 99.9256 | 99.7625 | 52.9997 | 13438 | 10 | 13443 | 32 | 31 | 96.8750 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.6664 | 95.9541 | 99.4410 | 50.6296 | 5692 | 240 | 5692 | 32 | 30 | 93.7500 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.8506 | 94.9010 | 98.8819 | 51.0518 | 2829 | 152 | 2830 | 32 | 27 | 84.3750 | |
| bgallagher-sentieon | SNP | ti | map_l250_m0_e0 | het | 97.6670 | 98.6081 | 96.7437 | 93.8565 | 921 | 13 | 921 | 31 | 5 | 16.1290 | |
| bgallagher-sentieon | SNP | tv | * | homalt | 99.9838 | 99.9759 | 99.9918 | 19.9074 | 377032 | 91 | 377017 | 31 | 25 | 80.6452 | |
| bgallagher-sentieon | SNP | tv | map_l250_m0_e0 | * | 97.0246 | 98.0392 | 96.0307 | 93.0983 | 750 | 15 | 750 | 31 | 5 | 16.1290 | |
| asubramanian-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.7580 | 97.6793 | 97.8367 | 88.4863 | 1389 | 33 | 1402 | 31 | 10 | 32.2581 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.5221 | 95.5960 | 99.5274 | 32.5866 | 6512 | 300 | 6529 | 31 | 31 | 100.0000 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.3955 | 88.2236 | 96.9815 | 64.0909 | 884 | 118 | 996 | 31 | 27 | 87.0968 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.8836 | 92.6404 | 99.3621 | 26.9063 | 4305 | 342 | 4829 | 31 | 30 | 96.7742 | |
| asubramanian-gatk | INDEL | I1_5 | map_siren | * | 93.2137 | 88.1864 | 98.8489 | 83.6431 | 2650 | 355 | 2662 | 31 | 7 | 22.5806 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.8703 | 95.1801 | 98.6216 | 73.1527 | 1876 | 95 | 2218 | 31 | 19 | 61.2903 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.8703 | 95.1801 | 98.6216 | 73.1527 | 1876 | 95 | 2218 | 31 | 19 | 61.2903 | |
| anovak-vg | INDEL | I1_5 | map_l250_m1_e0 | homalt | 69.3408 | 88.6364 | 56.9444 | 94.4573 | 39 | 5 | 41 | 31 | 28 | 90.3226 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 37.4335 | 27.0492 | 60.7595 | 65.3509 | 33 | 89 | 48 | 31 | 14 | 45.1613 | |
| astatham-gatk | INDEL | * | map_l150_m1_e0 | het | 95.3423 | 94.3860 | 96.3183 | 91.2356 | 807 | 48 | 811 | 31 | 4 | 12.9032 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.7010 | 99.6632 | 99.7389 | 50.8366 | 11835 | 40 | 11840 | 31 | 16 | 51.6129 | |
| astatham-gatk | INDEL | D1_5 | map_l100_m1_e0 | * | 97.1552 | 96.0498 | 98.2863 | 84.7368 | 1775 | 73 | 1778 | 31 | 6 | 19.3548 | |
| astatham-gatk | INDEL | D1_5 | map_l100_m2_e0 | * | 97.1748 | 96.0313 | 98.3458 | 85.2927 | 1839 | 76 | 1843 | 31 | 6 | 19.3548 | |
| astatham-gatk | INDEL | D1_5 | map_l100_m2_e1 | * | 97.1296 | 95.9257 | 98.3641 | 85.3950 | 1860 | 79 | 1864 | 31 | 6 | 19.3548 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.9798 | 94.5444 | 99.5441 | 27.3611 | 6724 | 388 | 6768 | 31 | 30 | 96.7742 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.9771 | 94.5358 | 99.5479 | 27.9803 | 6782 | 392 | 6826 | 31 | 30 | 96.7742 | |
| anovak-vg | INDEL | C1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 0.0000 | 0.0000 | 24.3902 | 79.5000 | 0 | 1 | 10 | 31 | 0 | 0.0000 | |
| anovak-vg | INDEL | C1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 0.0000 | 0.0000 | 22.5000 | 78.2609 | 0 | 1 | 9 | 31 | 0 | 0.0000 | |
| anovak-vg | INDEL | C6_15 | HG002compoundhet | * | 0.0000 | 0.0000 | 8.8235 | 73.0159 | 0 | 0 | 3 | 31 | 4 | 12.9032 | |
| anovak-vg | INDEL | C6_15 | HG002compoundhet | het | 0.0000 | 0.0000 | 8.8235 | 71.9008 | 0 | 0 | 3 | 31 | 4 | 12.9032 | |