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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
43651-43700 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | SNP | ti | map_l125_m2_e0 | * | 99.4203 | 99.4745 | 99.3661 | 73.2412 | 30099 | 159 | 30095 | 192 | 23 | 11.9792 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 98.4312 | 98.2694 | 98.5935 | 73.2405 | 2101 | 37 | 2103 | 30 | 18 | 60.0000 | |
| bgallagher-sentieon | SNP | * | map_l100_m0_e0 | het | 98.8545 | 99.3162 | 98.3971 | 73.2385 | 21060 | 145 | 21056 | 343 | 49 | 14.2857 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 93.7592 | 93.1507 | 94.3756 | 73.2357 | 1836 | 135 | 1829 | 109 | 67 | 61.4679 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 93.7592 | 93.1507 | 94.3756 | 73.2357 | 1836 | 135 | 1829 | 109 | 67 | 61.4679 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.6491 | 95.3947 | 95.9048 | 73.2348 | 2030 | 98 | 2014 | 86 | 77 | 89.5349 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 96.5360 | 94.4171 | 98.7522 | 73.2347 | 575 | 34 | 554 | 7 | 4 | 57.1429 | |
| egarrison-hhga | SNP | ti | map_l150_m2_e1 | homalt | 99.7853 | 99.6620 | 99.9088 | 73.2343 | 7667 | 26 | 7667 | 7 | 7 | 100.0000 | |
| hfeng-pmm2 | SNP | ti | map_l150_m2_e1 | homalt | 99.8050 | 99.8180 | 99.7921 | 73.2339 | 7679 | 14 | 7679 | 16 | 7 | 43.7500 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.6964 | 95.4417 | 95.9524 | 73.2314 | 2031 | 97 | 2015 | 85 | 77 | 90.5882 | |
| raldana-dualsentieon | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.6501 | 96.3918 | 98.9418 | 73.2295 | 374 | 14 | 374 | 4 | 3 | 75.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.6094 | 95.5357 | 95.6831 | 73.2283 | 2033 | 95 | 2017 | 91 | 76 | 83.5165 | |
| gduggal-snapvard | SNP | * | map_l150_m2_e1 | homalt | 97.6681 | 95.6963 | 99.7228 | 73.2280 | 11318 | 509 | 11153 | 31 | 25 | 80.6452 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 88.5500 | 89.5115 | 87.6089 | 73.2264 | 3243 | 380 | 3217 | 455 | 346 | 76.0440 | |
| jli-custom | SNP | ti | map_l150_m2_e1 | * | 99.2158 | 98.9046 | 99.5289 | 73.2251 | 20496 | 227 | 20494 | 97 | 36 | 37.1134 | |
| hfeng-pmm2 | SNP | * | map_l100_m0_e0 | het | 99.0069 | 99.2124 | 98.8022 | 73.2241 | 21038 | 167 | 21034 | 255 | 23 | 9.0196 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 95.1923 | 92.5234 | 98.0198 | 73.2238 | 495 | 40 | 495 | 10 | 10 | 100.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | * | homalt | 97.0923 | 98.3985 | 95.8203 | 73.2208 | 1536 | 25 | 1536 | 67 | 60 | 89.5522 | |
| ltrigg-rtg1 | INDEL | I1_5 | map_l100_m0_e0 | het | 95.5404 | 92.0245 | 99.3355 | 73.2206 | 300 | 26 | 299 | 2 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.0480 | 100.0000 | 96.1708 | 73.2150 | 653 | 0 | 653 | 26 | 25 | 96.1538 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.0480 | 100.0000 | 96.1708 | 73.2150 | 653 | 0 | 653 | 26 | 25 | 96.1538 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 75.8539 | 63.8889 | 93.3333 | 73.2143 | 69 | 39 | 70 | 5 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.4449 | 99.3179 | 97.5871 | 73.2136 | 728 | 5 | 728 | 18 | 14 | 77.7778 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 86.2310 | 89.4309 | 83.2523 | 73.2130 | 1210 | 143 | 1198 | 241 | 178 | 73.8589 | |
| hfeng-pmm1 | SNP | ti | map_l150_m2_e0 | homalt | 99.7833 | 99.7637 | 99.8030 | 73.2106 | 7598 | 18 | 7598 | 15 | 6 | 40.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.3958 | 98.0100 | 98.7847 | 73.2093 | 591 | 12 | 569 | 7 | 3 | 42.8571 | |
| ckim-dragen | SNP | ti | map_l100_m2_e1 | het | 98.1227 | 99.2603 | 97.0108 | 73.2091 | 30731 | 229 | 30734 | 947 | 88 | 9.2925 | |
| gduggal-snapvard | SNP | ti | map_l150_m2_e0 | homalt | 97.6054 | 95.6014 | 99.6952 | 73.2059 | 7281 | 335 | 7195 | 22 | 18 | 81.8182 | |
| ckim-isaac | SNP | tv | map_l100_m0_e0 | het | 74.7468 | 59.7757 | 99.7229 | 73.2042 | 4317 | 2905 | 4319 | 12 | 3 | 25.0000 | |
| gduggal-bwafb | SNP | * | map_l100_m0_e0 | het | 98.3117 | 98.5852 | 98.0398 | 73.2020 | 20905 | 300 | 20906 | 418 | 97 | 23.2057 | |
| eyeh-varpipe | SNP | ti | map_l125_m1_e0 | * | 99.2923 | 99.6523 | 98.9350 | 73.2001 | 29233 | 102 | 28704 | 309 | 21 | 6.7961 | |
| jli-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4538 | 99.1867 | 99.7223 | 73.1991 | 63907 | 524 | 63923 | 178 | 156 | 87.6404 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.9787 | 98.4234 | 99.5402 | 73.1978 | 437 | 7 | 433 | 2 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | I6_15 | HG002compoundhet | het | 93.1013 | 92.3077 | 93.9086 | 73.1973 | 192 | 16 | 185 | 12 | 6 | 50.0000 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 96.2638 | 96.1738 | 96.3539 | 73.1963 | 1483 | 59 | 1797 | 68 | 52 | 76.4706 | |
| gduggal-bwaplat | INDEL | D6_15 | * | het | 87.6003 | 79.2874 | 97.8603 | 73.1960 | 9191 | 2401 | 9193 | 201 | 85 | 42.2886 | |
| asubramanian-gatk | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 73.1959 | 0 | 0 | 0 | 26 | 0 | 0.0000 | ||
| astatham-gatk | INDEL | D16_PLUS | HG002compoundhet | homalt | 47.0588 | 100.0000 | 30.7692 | 73.1959 | 8 | 0 | 8 | 18 | 18 | 100.0000 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.9478 | 97.9351 | 97.9605 | 73.1911 | 5976 | 126 | 5956 | 124 | 48 | 38.7097 | |
| hfeng-pmm2 | SNP | ti | map_l150_m2_e0 | homalt | 99.8031 | 99.8162 | 99.7900 | 73.1902 | 7602 | 14 | 7602 | 16 | 7 | 43.7500 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 90.7855 | 83.8319 | 98.9970 | 73.1888 | 3251 | 627 | 3257 | 33 | 8 | 24.2424 | |
| cchapple-custom | SNP | tv | map_l150_m0_e0 | homalt | 97.4517 | 95.0301 | 100.0000 | 73.1873 | 1262 | 66 | 1261 | 0 | 0 | ||
| gduggal-snapvard | SNP | * | map_l150_m2_e0 | homalt | 97.6688 | 95.7005 | 99.7199 | 73.1870 | 11196 | 503 | 11035 | 31 | 25 | 80.6452 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 92.1761 | 97.7083 | 87.2368 | 73.1862 | 1407 | 33 | 1367 | 200 | 4 | 2.0000 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.6301 | 95.4887 | 95.7720 | 73.1847 | 2032 | 96 | 2016 | 89 | 78 | 87.6404 | |
| ciseli-custom | SNP | * | map_l150_m2_e1 | homalt | 86.5594 | 84.7045 | 88.4973 | 73.1841 | 10018 | 1809 | 9994 | 1299 | 1047 | 80.6005 | |
| egarrison-hhga | SNP | ti | map_l150_m2_e0 | homalt | 99.7831 | 99.6586 | 99.9079 | 73.1839 | 7590 | 26 | 7590 | 7 | 7 | 100.0000 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 96.3424 | 97.9964 | 94.7434 | 73.1789 | 538 | 11 | 757 | 42 | 37 | 88.0952 | |
| cchapple-custom | SNP | * | map_l125_m1_e0 | * | 96.8884 | 97.0680 | 96.7095 | 73.1758 | 43998 | 1329 | 43998 | 1497 | 343 | 22.9125 | |
| ciseli-custom | SNP | * | map_l150_m2_e0 | homalt | 86.5638 | 84.7166 | 88.4932 | 73.1740 | 9911 | 1788 | 9890 | 1286 | 1036 | 80.5599 | |