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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
18801-18850 / 86044 show all | |||||||||||||||
| astatham-gatk | INDEL | D1_5 | map_l125_m2_e0 | * | 96.9583 | 96.1505 | 97.7798 | 88.0289 | 1099 | 44 | 1101 | 25 | 5 | 20.0000 | |
| astatham-gatk | INDEL | D1_5 | map_l125_m2_e1 | * | 96.9505 | 96.1106 | 97.8051 | 88.0870 | 1112 | 45 | 1114 | 25 | 5 | 20.0000 | |
| astatham-gatk | INDEL | D6_15 | HG002complexvar | het | 99.0140 | 98.8462 | 99.1825 | 59.3945 | 3084 | 36 | 3033 | 25 | 19 | 76.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0053 | 96.4936 | 99.5651 | 50.8758 | 5724 | 208 | 5724 | 25 | 23 | 92.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 94.4072 | 100.0000 | 89.4068 | 69.3904 | 211 | 0 | 211 | 25 | 24 | 96.0000 | |
| asubramanian-gatk | SNP | tv | * | hetalt | 95.7533 | 94.4891 | 97.0519 | 45.7454 | 823 | 48 | 823 | 25 | 2 | 8.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | HG002compoundhet | homalt | 39.0244 | 100.0000 | 24.2424 | 67.9612 | 8 | 0 | 8 | 25 | 25 | 100.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.0769 | 99.5816 | 96.6171 | 61.4099 | 714 | 3 | 714 | 25 | 24 | 96.0000 | |
| anovak-vg | INDEL | C1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 28.5714 | 100.0000 | 16.6667 | 92.7361 | 1 | 0 | 5 | 25 | 0 | 0.0000 | |
| anovak-vg | INDEL | C1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 24.2424 | 100.0000 | 13.7931 | 91.4454 | 1 | 0 | 4 | 25 | 0 | 0.0000 | |
| anovak-vg | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 0.0000 | 0.0000 | 88.6878 | 0 | 0 | 0 | 25 | 3 | 12.0000 | ||
| anovak-vg | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 0.0000 | 0.0000 | 88.1517 | 0 | 0 | 0 | 25 | 3 | 12.0000 | ||
| anovak-vg | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 0.0000 | 0.0000 | 88.6878 | 0 | 0 | 0 | 25 | 3 | 12.0000 | ||
| anovak-vg | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 0.0000 | 0.0000 | 88.1517 | 0 | 0 | 0 | 25 | 3 | 12.0000 | ||
| anovak-vg | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 57.5634 | 52.4590 | 63.7681 | 43.4426 | 32 | 29 | 44 | 25 | 20 | 80.0000 | |
| anovak-vg | INDEL | D6_15 | map_l125_m2_e0 | * | 76.3127 | 73.8095 | 78.9916 | 88.9713 | 93 | 33 | 94 | 25 | 15 | 60.0000 | |
| anovak-vg | INDEL | D6_15 | map_l125_m2_e1 | * | 76.3524 | 73.4375 | 79.5082 | 88.8584 | 94 | 34 | 97 | 25 | 15 | 60.0000 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 27.6316 | 37.5000 | 21.8750 | 57.3333 | 6 | 10 | 7 | 25 | 17 | 68.0000 | |
| astatham-gatk | SNP | tv | HG002complexvar | het | 98.5778 | 97.2116 | 99.9829 | 21.9634 | 146528 | 4203 | 146456 | 25 | 11 | 44.0000 | |
| astatham-gatk | SNP | tv | map_l250_m1_e0 | * | 92.5829 | 87.0042 | 98.9261 | 90.0355 | 2303 | 344 | 2303 | 25 | 7 | 28.0000 | |
| astatham-gatk | SNP | tv | map_l250_m2_e0 | * | 92.3931 | 86.6065 | 99.0083 | 90.6397 | 2496 | 386 | 2496 | 25 | 7 | 28.0000 | |
| astatham-gatk | SNP | tv | map_l250_m2_e1 | * | 92.4090 | 86.6255 | 99.0200 | 90.7000 | 2526 | 390 | 2526 | 25 | 7 | 28.0000 | |
| asubramanian-gatk | INDEL | C16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 0.0000 | 0.0000 | 85.7955 | 0 | 0 | 0 | 25 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | D16_PLUS | HG002compoundhet | homalt | 39.0244 | 100.0000 | 24.2424 | 68.2692 | 8 | 0 | 8 | 25 | 23 | 92.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.8376 | 96.7213 | 94.9698 | 72.2501 | 472 | 16 | 472 | 25 | 21 | 84.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.3721 | 98.1869 | 96.5706 | 61.2646 | 704 | 13 | 704 | 25 | 22 | 88.0000 | |
| anovak-vg | INDEL | I1_5 | map_l250_m1_e0 | het | 47.9644 | 43.3333 | 53.7037 | 97.5785 | 26 | 34 | 29 | 25 | 3 | 12.0000 | |
| anovak-vg | INDEL | I1_5 | map_l250_m2_e0 | het | 50.5360 | 45.4545 | 56.8966 | 97.6697 | 30 | 36 | 33 | 25 | 3 | 12.0000 | |
| anovak-vg | INDEL | I1_5 | map_l250_m2_e1 | het | 50.5360 | 45.4545 | 56.8966 | 97.7255 | 30 | 36 | 33 | 25 | 3 | 12.0000 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 97.8522 | 97.4079 | 98.3005 | 42.9181 | 1428 | 38 | 1446 | 25 | 22 | 88.0000 | |
| bgallagher-sentieon | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.4931 | 99.5753 | 99.4111 | 78.7569 | 4220 | 18 | 4220 | 25 | 5 | 20.0000 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 93.7644 | 99.0244 | 89.0351 | 90.6863 | 203 | 2 | 203 | 25 | 23 | 92.0000 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.6270 | 99.8753 | 99.3798 | 50.2161 | 4006 | 5 | 4006 | 25 | 1 | 4.0000 | |
| jli-custom | INDEL | * | map_l125_m2_e0 | * | 98.5850 | 98.3151 | 98.8564 | 86.6789 | 2159 | 37 | 2161 | 25 | 8 | 32.0000 | |
| jli-custom | INDEL | * | map_l125_m2_e1 | * | 98.5806 | 98.2921 | 98.8708 | 86.7884 | 2187 | 38 | 2189 | 25 | 8 | 32.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.8615 | 94.2539 | 99.6175 | 50.6158 | 6512 | 397 | 6511 | 25 | 20 | 80.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6812 | 95.9164 | 99.5121 | 62.7887 | 5097 | 217 | 5099 | 25 | 19 | 76.0000 | |
| hfeng-pmm3 | SNP | * | HG002complexvar | homalt | 99.9822 | 99.9730 | 99.9913 | 19.9554 | 288496 | 78 | 288478 | 25 | 24 | 96.0000 | |
| hfeng-pmm2 | INDEL | D16_PLUS | HG002complexvar | * | 96.3580 | 94.4005 | 98.3985 | 65.2184 | 1551 | 92 | 1536 | 25 | 15 | 60.0000 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.4316 | 96.3170 | 98.5722 | 66.0922 | 1726 | 66 | 1726 | 25 | 17 | 68.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 81.2500 | 70.8752 | 95.1830 | 49.0677 | 494 | 203 | 494 | 25 | 23 | 92.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l125_m1_e0 | het | 97.8277 | 99.0358 | 96.6488 | 86.8244 | 719 | 7 | 721 | 25 | 2 | 8.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l125_m2_e0 | het | 97.9343 | 99.0838 | 96.8112 | 87.3344 | 757 | 7 | 759 | 25 | 2 | 8.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l125_m2_e1 | het | 97.9502 | 99.0909 | 96.8354 | 87.4264 | 763 | 7 | 765 | 25 | 2 | 8.0000 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 89.6142 | 93.7888 | 85.7955 | 36.9176 | 151 | 10 | 151 | 25 | 25 | 100.0000 | |
| hfeng-pmm2 | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.8844 | 98.3152 | 99.4603 | 36.9967 | 4610 | 79 | 4607 | 25 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | tv | map_l250_m0_e0 | * | 97.4026 | 98.0392 | 96.7742 | 93.4737 | 750 | 15 | 750 | 25 | 4 | 16.0000 | |
| hfeng-pmm3 | INDEL | * | map_l150_m1_e0 | * | 98.2484 | 98.3558 | 98.1413 | 87.8949 | 1316 | 22 | 1320 | 25 | 6 | 24.0000 | |
| hfeng-pmm3 | INDEL | * | map_l150_m2_e0 | * | 98.2631 | 98.2955 | 98.2307 | 88.7365 | 1384 | 24 | 1388 | 25 | 6 | 24.0000 | |
| hfeng-pmm3 | INDEL | * | map_l150_m2_e1 | * | 98.1943 | 98.1237 | 98.2651 | 88.7746 | 1412 | 27 | 1416 | 25 | 6 | 24.0000 | |