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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
19251-19300 / 86044 show all | |||||||||||||||
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.7357 | 95.1299 | 98.3966 | 42.6150 | 1172 | 60 | 1166 | 19 | 9 | 47.3684 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 0.0000 | 92.4338 | 0.0000 | 0.0000 | 733 | 60 | 0 | 0 | 0 | ||
| cchapple-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.1585 | 96.0784 | 98.2630 | 83.6495 | 1470 | 60 | 1584 | 28 | 20 | 71.4286 | |
| cchapple-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.1585 | 96.0784 | 98.2630 | 83.6495 | 1470 | 60 | 1584 | 28 | 20 | 71.4286 | |
| ckim-gatk | INDEL | D1_5 | HG002complexvar | het | 99.7759 | 99.7111 | 99.8409 | 56.3066 | 20705 | 60 | 20710 | 33 | 15 | 45.4545 | |
| ckim-dragen | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.7395 | 97.7629 | 99.7358 | 42.4788 | 2622 | 60 | 2643 | 7 | 7 | 100.0000 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.3148 | 95.4405 | 99.2642 | 37.6033 | 1235 | 59 | 1349 | 10 | 10 | 100.0000 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.1021 | 88.9925 | 97.6096 | 61.2654 | 477 | 59 | 490 | 12 | 11 | 91.6667 | |
| ciseli-custom | INDEL | * | map_l250_m2_e0 | homalt | 59.5745 | 48.6957 | 76.7123 | 96.9159 | 56 | 59 | 56 | 17 | 11 | 64.7059 | |
| ciseli-custom | INDEL | * | map_l250_m2_e1 | homalt | 60.0000 | 49.1379 | 77.0270 | 96.9384 | 57 | 59 | 57 | 17 | 11 | 64.7059 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.5044 | 99.4538 | 99.5551 | 80.0137 | 10742 | 59 | 10742 | 48 | 17 | 35.4167 | |
| ckim-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7872 | 99.6565 | 99.9183 | 57.2121 | 17118 | 59 | 17114 | 14 | 8 | 57.1429 | |
| ciseli-custom | INDEL | D16_PLUS | map_l100_m2_e0 | * | 44.1674 | 34.4444 | 61.5385 | 89.4737 | 31 | 59 | 32 | 20 | 14 | 70.0000 | |
| ciseli-custom | INDEL | D6_15 | map_l125_m2_e1 | * | 55.2000 | 53.9062 | 56.5574 | 92.2687 | 69 | 59 | 69 | 53 | 29 | 54.7170 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 59 | 0 | 0 | 0 | |||
| ckim-gatk | INDEL | * | HG002compoundhet | het | 93.4586 | 98.5589 | 88.8602 | 79.6039 | 4035 | 59 | 3789 | 475 | 465 | 97.8947 | |
| ckim-gatk | INDEL | * | map_l100_m2_e0 | * | 97.0660 | 98.4024 | 95.7654 | 89.0665 | 3634 | 59 | 3641 | 161 | 20 | 12.4224 | |
| cchapple-custom | INDEL | I16_PLUS | * | het | 98.4654 | 97.8293 | 99.1099 | 69.2948 | 2659 | 59 | 5122 | 46 | 28 | 60.8696 | |
| astatham-gatk | SNP | * | map_l250_m1_e0 | homalt | 98.6256 | 97.6045 | 99.6683 | 85.3151 | 2404 | 59 | 2404 | 8 | 7 | 87.5000 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.7920 | 99.4303 | 96.2068 | 45.3054 | 10298 | 59 | 10906 | 430 | 320 | 74.4186 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.3254 | 96.9477 | 97.7059 | 65.2032 | 1874 | 59 | 1874 | 44 | 43 | 97.7273 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 59 | 0 | 0 | 0 | |||
| bgallagher-sentieon | SNP | tv | map_l125_m1_e0 | het | 98.8364 | 99.4173 | 98.2622 | 74.9493 | 10067 | 59 | 10065 | 178 | 22 | 12.3596 | |
| bgallagher-sentieon | SNP | tv | map_l125_m2_e0 | het | 98.8667 | 99.4350 | 98.3049 | 76.2296 | 10383 | 59 | 10381 | 179 | 22 | 12.2905 | |
| bgallagher-sentieon | SNP | tv | map_l125_m2_e1 | het | 98.8786 | 99.4409 | 98.3226 | 76.2835 | 10494 | 59 | 10492 | 179 | 22 | 12.2905 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.1381 | 98.8474 | 99.4304 | 72.0835 | 5060 | 59 | 5237 | 30 | 24 | 80.0000 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 37.5202 | 27.1605 | 60.6557 | 60.8974 | 22 | 59 | 37 | 24 | 17 | 70.8333 | |
| anovak-vg | INDEL | I6_15 | map_l100_m2_e0 | * | 53.4759 | 49.1379 | 58.6538 | 81.9130 | 57 | 59 | 61 | 43 | 25 | 58.1395 | |
| anovak-vg | INDEL | I6_15 | map_l100_m2_e1 | * | 53.2425 | 49.1379 | 58.0952 | 82.0819 | 57 | 59 | 61 | 44 | 25 | 56.8182 | |
| anovak-vg | INDEL | I6_15 | segdup | het | 38.0775 | 28.9157 | 55.7377 | 91.0688 | 24 | 59 | 34 | 27 | 13 | 48.1481 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 96.2004 | 96.2658 | 96.1350 | 51.4737 | 1521 | 59 | 1567 | 63 | 25 | 39.6825 | |
| asubramanian-gatk | INDEL | D1_5 | HG002compoundhet | het | 95.2389 | 96.5856 | 93.9292 | 78.7201 | 1669 | 59 | 1671 | 108 | 103 | 95.3704 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.3602 | 96.1713 | 98.5789 | 73.8003 | 1482 | 59 | 1873 | 27 | 17 | 62.9630 | |
| asubramanian-gatk | SNP | ti | func_cds | * | 99.6805 | 99.5721 | 99.7892 | 27.6472 | 13728 | 59 | 13726 | 29 | 1 | 3.4483 | |
| jmaeng-gatk | SNP | tv | segdup | * | 98.1687 | 99.3085 | 97.0548 | 94.6921 | 8473 | 59 | 8469 | 257 | 8 | 3.1128 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | * | homalt | 98.0769 | 96.5130 | 99.6923 | 55.5890 | 1633 | 59 | 1620 | 5 | 5 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.4377 | 95.6458 | 99.2980 | 71.4667 | 1296 | 59 | 1273 | 9 | 4 | 44.4444 | |
| ltrigg-rtg1 | INDEL | D1_5 | HG002compoundhet | het | 96.9264 | 96.5856 | 97.2696 | 68.4720 | 1669 | 59 | 1710 | 48 | 21 | 43.7500 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 85.9727 | 76.0163 | 98.9305 | 71.6667 | 187 | 59 | 185 | 2 | 0 | 0.0000 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 94.7936 | 91.4119 | 98.4351 | 78.0939 | 628 | 59 | 629 | 10 | 5 | 50.0000 | |
| jli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.3218 | 94.7834 | 100.0000 | 40.0222 | 1072 | 59 | 1079 | 0 | 0 | ||
| ltrigg-rtg1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.3750 | 99.1428 | 97.6190 | 80.4477 | 6824 | 59 | 6847 | 167 | 2 | 1.1976 | |
| ltrigg-rtg1 | SNP | * | map_l125_m1_e0 | homalt | 99.7779 | 99.6510 | 99.9051 | 65.6341 | 16846 | 59 | 16847 | 16 | 16 | 100.0000 | |
| ltrigg-rtg1 | SNP | * | map_l125_m2_e0 | homalt | 99.7839 | 99.6604 | 99.9077 | 68.1589 | 17316 | 59 | 17317 | 16 | 16 | 100.0000 | |
| ltrigg-rtg1 | SNP | * | map_l125_m2_e1 | homalt | 99.7859 | 99.6635 | 99.9086 | 68.1960 | 17473 | 59 | 17480 | 16 | 16 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 95.3619 | 93.9050 | 96.8649 | 73.4043 | 909 | 59 | 896 | 29 | 7 | 24.1379 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 0.0000 | 3.2787 | 0.0000 | 0.0000 | 2 | 59 | 0 | 0 | 0 | ||
| raldana-dualsentieon | SNP | tv | map_l150_m0_e0 | het | 98.1142 | 97.9247 | 98.3045 | 80.9258 | 2784 | 59 | 2783 | 48 | 1 | 2.0833 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.3392 | 99.0283 | 99.6520 | 55.6062 | 6013 | 59 | 6013 | 21 | 19 | 90.4762 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.8135 | 98.9459 | 94.7711 | 71.2462 | 5538 | 59 | 5528 | 305 | 297 | 97.3770 | |