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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
19101-19150 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9345 | 98.2816 | 99.5962 | 71.4015 | 92826 | 1623 | 92734 | 376 | 307 | 81.6489 | |
| cchapple-custom | INDEL | D1_5 | segdup | het | 99.1458 | 98.6994 | 99.5962 | 94.5834 | 683 | 9 | 740 | 3 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.5308 | 95.5496 | 99.5959 | 50.2969 | 5668 | 264 | 5668 | 23 | 21 | 91.3043 | |
| ltrigg-rtg2 | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.2967 | 98.9992 | 99.5959 | 61.6070 | 9595 | 97 | 9613 | 39 | 5 | 12.8205 | |
| jmaeng-gatk | INDEL | D6_15 | HG002compoundhet | hetalt | 96.5549 | 93.6940 | 99.5959 | 24.0546 | 7637 | 514 | 7641 | 31 | 31 | 100.0000 | |
| ckim-dragen | INDEL | D6_15 | HG002compoundhet | hetalt | 96.5353 | 93.6572 | 99.5958 | 23.6915 | 7634 | 517 | 7638 | 31 | 31 | 100.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.2713 | 96.9816 | 99.5957 | 64.0330 | 739 | 23 | 739 | 3 | 0 | 0.0000 | |
| ndellapenna-hhga | SNP | * | map_l125_m0_e0 | het | 98.3855 | 97.2047 | 99.5955 | 74.1909 | 12310 | 354 | 12310 | 50 | 23 | 46.0000 | |
| astatham-gatk | SNP | ti | map_l150_m1_e0 | het | 85.9873 | 75.6508 | 99.5954 | 82.9552 | 9358 | 3012 | 9354 | 38 | 18 | 47.3684 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.4072 | 95.3136 | 99.5949 | 50.5186 | 5654 | 278 | 5654 | 23 | 21 | 91.3043 | |
| ltrigg-rtg1 | SNP | * | map_l250_m0_e0 | * | 95.7430 | 92.1780 | 99.5949 | 87.5418 | 1968 | 167 | 1967 | 8 | 3 | 37.5000 | |
| jli-custom | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.6524 | 99.7101 | 99.5947 | 36.6587 | 3440 | 10 | 3440 | 14 | 2 | 14.2857 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.4660 | 99.3376 | 99.5947 | 73.4410 | 3599 | 24 | 3686 | 15 | 12 | 80.0000 | |
| ckim-dragen | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.2554 | 98.9184 | 99.5947 | 75.9330 | 6585 | 72 | 6635 | 27 | 13 | 48.1481 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5943 | 99.5943 | 99.5943 | 58.4317 | 491 | 2 | 491 | 2 | 0 | 0.0000 | |
| ckim-gatk | INDEL | D1_5 | HG002compoundhet | hetalt | 96.5709 | 93.7255 | 99.5943 | 58.2762 | 9575 | 641 | 9575 | 39 | 39 | 100.0000 | |
| ckim-isaac | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.5585 | 93.7023 | 99.5943 | 53.9683 | 491 | 33 | 491 | 2 | 1 | 50.0000 | |
| ckim-vqsr | INDEL | D1_5 | HG002compoundhet | hetalt | 96.5656 | 93.7157 | 99.5943 | 58.2787 | 9574 | 642 | 9574 | 39 | 39 | 100.0000 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 93.4546 | 88.0282 | 99.5940 | 77.7945 | 750 | 102 | 736 | 3 | 3 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | * | het | 98.8597 | 98.1362 | 99.5939 | 56.2294 | 9846 | 187 | 9811 | 40 | 29 | 72.5000 | |
| ckim-dragen | SNP | tv | map_l125_m0_e0 | homalt | 99.4590 | 99.3246 | 99.5937 | 66.7118 | 2206 | 15 | 2206 | 9 | 7 | 77.7778 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.5583 | 99.5229 | 99.5937 | 62.9090 | 11055 | 53 | 11030 | 45 | 18 | 40.0000 | |
| ndellapenna-hhga | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5343 | 99.4751 | 99.5935 | 60.5291 | 10044 | 53 | 10045 | 41 | 39 | 95.1220 | |
| cchapple-custom | INDEL | D1_5 | map_l100_m0_e0 | homalt | 97.8280 | 96.1240 | 99.5935 | 81.4199 | 248 | 10 | 245 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l150_m2_e1 | homalt | 99.1903 | 98.7903 | 99.5935 | 86.5058 | 245 | 3 | 245 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l150_m2_e1 | homalt | 99.1903 | 98.7903 | 99.5935 | 85.8702 | 245 | 3 | 245 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 95.6093 | 91.9316 | 99.5935 | 30.0616 | 10209 | 896 | 10290 | 42 | 37 | 88.0952 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.4924 | 99.3915 | 99.5935 | 55.2320 | 490 | 3 | 490 | 2 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | I1_5 | * | * | 99.0996 | 98.6108 | 99.5933 | 59.2515 | 148571 | 2093 | 148648 | 607 | 454 | 74.7941 | |
| jli-custom | INDEL | D16_PLUS | HG002compoundhet | hetalt | 97.5241 | 95.5394 | 99.5931 | 24.6166 | 1842 | 86 | 1958 | 8 | 8 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | map_l250_m2_e0 | * | 56.1308 | 39.0775 | 99.5931 | 97.1311 | 1957 | 3051 | 1958 | 8 | 2 | 25.0000 | |
| egarrison-hhga | SNP | ti | HG002compoundhet | het | 98.7211 | 97.8643 | 99.5931 | 37.6968 | 9302 | 203 | 9300 | 38 | 21 | 55.2632 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.6460 | 99.6990 | 99.5931 | 55.9882 | 11262 | 34 | 11258 | 46 | 37 | 80.4348 | |
| jmaeng-gatk | INDEL | D1_5 | HG002compoundhet | hetalt | 96.4037 | 93.4123 | 99.5930 | 58.4493 | 9543 | 673 | 9543 | 39 | 39 | 100.0000 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.5883 | 90.0626 | 99.5930 | 87.0976 | 2447 | 270 | 2447 | 10 | 4 | 40.0000 | |
| jli-custom | INDEL | I1_5 | map_l125_m2_e0 | het | 98.8859 | 98.1891 | 99.5927 | 86.2696 | 488 | 9 | 489 | 2 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | tv | map_l250_m2_e0 | * | 28.9950 | 16.9674 | 99.5927 | 98.5624 | 489 | 2393 | 489 | 2 | 0 | 0.0000 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.5292 | 99.4658 | 99.5927 | 55.2671 | 3910 | 21 | 3912 | 16 | 4 | 25.0000 | |
| dgrover-gatk | SNP | ti | map_l100_m1_e0 | * | 99.5344 | 99.4763 | 99.5926 | 66.0277 | 47680 | 251 | 47673 | 195 | 49 | 25.1282 | |
| ckim-vqsr | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.3564 | 99.1213 | 99.5925 | 49.2504 | 2933 | 26 | 2933 | 12 | 3 | 25.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.7076 | 97.8383 | 99.5925 | 68.2618 | 1222 | 27 | 1222 | 5 | 3 | 60.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.7076 | 97.8383 | 99.5925 | 68.2618 | 1222 | 27 | 1222 | 5 | 3 | 60.0000 | |
| raldana-dualsentieon | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.5255 | 97.4811 | 99.5925 | 63.6357 | 4644 | 120 | 4644 | 19 | 2 | 10.5263 | |
| asubramanian-gatk | SNP | tv | map_l150_m0_e0 | * | 29.8574 | 17.5611 | 99.5924 | 97.2219 | 733 | 3441 | 733 | 3 | 1 | 33.3333 | |
| ckim-isaac | SNP | tv | HG002compoundhet | homalt | 88.3010 | 79.3093 | 99.5923 | 36.8889 | 2687 | 701 | 2687 | 11 | 11 | 100.0000 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 69.3783 | 53.2297 | 99.5922 | 52.1673 | 4450 | 3910 | 4396 | 18 | 16 | 88.8889 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 69.3783 | 53.2297 | 99.5922 | 52.1673 | 4450 | 3910 | 4396 | 18 | 16 | 88.8889 | |
| hfeng-pmm1 | SNP | * | map_l125_m1_e0 | het | 99.2507 | 98.9117 | 99.5921 | 70.2654 | 28083 | 309 | 28077 | 115 | 29 | 25.2174 | |
| hfeng-pmm1 | SNP | ti | map_l150_m1_e0 | * | 99.3490 | 99.1071 | 99.5921 | 73.5929 | 19536 | 176 | 19532 | 80 | 23 | 28.7500 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.2771 | 98.9642 | 99.5919 | 45.6545 | 11752 | 123 | 11714 | 48 | 17 | 35.4167 | |