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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
76751-76800 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5764 | 98.1511 | 99.0054 | 69.1058 | 19217 | 362 | 19211 | 193 | 36 | 18.6528 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5764 | 98.1511 | 99.0054 | 69.1058 | 19217 | 362 | 19211 | 193 | 36 | 18.6528 | |
| egarrison-hhga | SNP | * | map_l100_m0_e0 | * | 99.3454 | 98.8977 | 99.7972 | 67.0353 | 32479 | 362 | 32480 | 66 | 33 | 50.0000 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 84.3756 | 73.2446 | 99.4960 | 78.1450 | 991 | 362 | 987 | 5 | 3 | 60.0000 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.2755 | 0.0000 | 0.0000 | 1 | 362 | 0 | 0 | 0 | ||
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 81.5240 | 69.7071 | 98.1651 | 30.1282 | 833 | 362 | 535 | 10 | 10 | 100.0000 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 69.8290 | 73.2103 | 66.7462 | 59.7115 | 992 | 363 | 839 | 418 | 413 | 98.8038 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 92.0621 | 91.0745 | 93.0713 | 64.3876 | 3704 | 363 | 3694 | 275 | 266 | 96.7273 | |
| rpoplin-dv42 | SNP | * | map_l100_m0_e0 | * | 99.0394 | 98.8947 | 99.1845 | 66.6640 | 32478 | 363 | 32474 | 267 | 146 | 54.6816 | |
| jlack-gatk | INDEL | I16_PLUS | * | * | 95.3468 | 94.3077 | 96.4091 | 70.3461 | 6014 | 363 | 6014 | 224 | 155 | 69.1964 | |
| gduggal-snapvard | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 83.9078 | 94.1790 | 75.6567 | 81.6542 | 5873 | 363 | 5818 | 1872 | 118 | 6.3034 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 363 | 0 | 0 | 0 | |||
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 363 | 0 | 0 | 0 | |||
| ckim-isaac | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 93.8020 | 94.0511 | 93.5541 | 72.2618 | 5739 | 363 | 5762 | 397 | 212 | 53.4005 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 85.6262 | 97.1009 | 76.5768 | 51.4227 | 12158 | 363 | 12930 | 3955 | 3851 | 97.3704 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.8071 | 93.8433 | 99.9643 | 38.7051 | 5533 | 363 | 5593 | 2 | 2 | 100.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.8071 | 93.8433 | 99.9643 | 38.7051 | 5533 | 363 | 5593 | 2 | 2 | 100.0000 | |
| cchapple-custom | INDEL | * | HG002complexvar | hetalt | 0.0000 | 90.1865 | 0.0000 | 0.0000 | 3336 | 363 | 0 | 0 | 0 | ||
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 88.1791 | 79.5031 | 98.9806 | 34.9542 | 1408 | 363 | 2039 | 21 | 15 | 71.4286 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | HG002compoundhet | hetalt | 90.2840 | 82.6087 | 99.5316 | 37.2520 | 1729 | 364 | 1700 | 8 | 8 | 100.0000 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 8.2305 | 5.2083 | 19.6078 | 88.3429 | 20 | 364 | 20 | 82 | 46 | 56.0976 | |
| gduggal-snapfb | SNP | * | map_l150_m0_e0 | het | 94.3991 | 95.4156 | 93.4040 | 78.0920 | 7576 | 364 | 7576 | 535 | 258 | 48.2243 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.9422 | 97.7317 | 98.1536 | 61.1398 | 15683 | 364 | 15682 | 295 | 284 | 96.2712 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 80.9161 | 72.4451 | 91.6304 | 55.0342 | 957 | 364 | 843 | 77 | 76 | 98.7013 | |
| gduggal-bwaplat | INDEL | * | map_l150_m2_e1 | het | 75.1678 | 60.6061 | 98.9399 | 96.4527 | 560 | 364 | 560 | 6 | 1 | 16.6667 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9618 | 96.7154 | 99.2407 | 47.8941 | 10718 | 364 | 10718 | 82 | 78 | 95.1220 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9752 | 96.7154 | 99.2683 | 46.8913 | 10718 | 364 | 10718 | 79 | 74 | 93.6709 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.6115 | 86.6324 | 99.4771 | 37.4276 | 2359 | 364 | 2473 | 13 | 12 | 92.3077 | |
| astatham-gatk | SNP | tv | map_l250_m2_e0 | het | 89.1403 | 81.2371 | 98.7469 | 92.0672 | 1576 | 364 | 1576 | 20 | 3 | 15.0000 | |
| jpowers-varprowl | SNP | tv | map_l100_m0_e0 | * | 96.7509 | 96.7160 | 96.7858 | 76.5215 | 10720 | 364 | 10720 | 356 | 89 | 25.0000 | |
| jpowers-varprowl | SNP | tv | map_l125_m2_e0 | het | 96.3204 | 96.5141 | 96.1274 | 80.0949 | 10078 | 364 | 10078 | 406 | 94 | 23.1527 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | * | * | 96.8429 | 94.6197 | 99.1732 | 57.6142 | 6419 | 365 | 6357 | 53 | 36 | 67.9245 | |
| ltrigg-rtg1 | SNP | tv | map_siren | * | 99.4402 | 99.2053 | 99.6762 | 52.0914 | 45565 | 365 | 45564 | 148 | 13 | 8.7838 | |
| ghariani-varprowl | SNP | * | map_l125_m0_e0 | * | 97.0458 | 98.1171 | 95.9976 | 79.8507 | 19020 | 365 | 19020 | 793 | 172 | 21.6898 | |
| raldana-dualsentieon | SNP | * | map_l100_m1_e0 | het | 99.0827 | 99.1953 | 98.9703 | 66.7199 | 44994 | 365 | 44983 | 468 | 7 | 1.4957 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.8703 | 98.0010 | 99.7551 | 37.4155 | 17894 | 365 | 17924 | 44 | 41 | 93.1818 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | * | hetalt | 90.2131 | 82.6025 | 99.3685 | 50.0717 | 1733 | 365 | 1731 | 11 | 11 | 100.0000 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.4525 | 98.8280 | 98.0798 | 67.6014 | 30778 | 365 | 31005 | 607 | 33 | 5.4366 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.4525 | 98.8280 | 98.0798 | 67.6014 | 30778 | 365 | 31005 | 607 | 33 | 5.4366 | |
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.3012 | 97.9926 | 98.6117 | 39.2636 | 17818 | 365 | 17829 | 251 | 187 | 74.5020 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.0259 | 90.8384 | 97.4454 | 47.9934 | 3619 | 365 | 3700 | 97 | 76 | 78.3505 | |
| anovak-vg | INDEL | * | map_l150_m2_e1 | * | 72.7945 | 74.6352 | 71.0425 | 90.5099 | 1074 | 365 | 1104 | 450 | 242 | 53.7778 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.2898 | 93.2880 | 99.4913 | 26.4604 | 5073 | 365 | 5085 | 26 | 21 | 80.7692 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 73.8957 | 69.0940 | 79.4146 | 45.3333 | 816 | 365 | 814 | 211 | 209 | 99.0521 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.8058 | 93.8094 | 100.0000 | 40.1072 | 5531 | 365 | 5588 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.8058 | 93.8094 | 100.0000 | 40.1072 | 5531 | 365 | 5588 | 0 | 0 | ||
| dgrover-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.7887 | 96.0736 | 99.5661 | 64.7766 | 8931 | 365 | 8950 | 39 | 38 | 97.4359 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 79.6299 | 72.3065 | 88.6040 | 54.8263 | 953 | 365 | 933 | 120 | 112 | 93.3333 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 95.8906 | 94.5652 | 97.2537 | 40.0019 | 6351 | 365 | 6268 | 177 | 104 | 58.7571 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.8065 | 98.5086 | 99.1063 | 41.3831 | 24174 | 366 | 24176 | 218 | 209 | 95.8716 | |