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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
73051-73100 / 86044 show all | |||||||||||||||
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.6497 | 97.9456 | 99.3640 | 46.2896 | 1621 | 34 | 2812 | 18 | 16 | 88.8889 | |
| cchapple-custom | INDEL | I1_5 | HG002complexvar | * | 99.1800 | 98.7291 | 99.6350 | 52.8581 | 32939 | 424 | 31939 | 117 | 104 | 88.8889 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.4329 | 96.3492 | 98.5413 | 62.2630 | 607 | 23 | 608 | 9 | 8 | 88.8889 | |
| jpowers-varprowl | INDEL | D16_PLUS | segdup | * | 80.4978 | 77.5862 | 83.6364 | 94.2827 | 45 | 13 | 46 | 9 | 8 | 88.8889 | |
| jpowers-varprowl | INDEL | D16_PLUS | segdup | het | 86.6873 | 94.5946 | 80.0000 | 94.4030 | 35 | 2 | 36 | 9 | 8 | 88.8889 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 43.7158 | 29.2554 | 86.4426 | 46.4806 | 1497 | 3620 | 1492 | 234 | 208 | 88.8889 | |
| ltrigg-rtg1 | INDEL | D6_15 | HG002compoundhet | homalt | 80.0000 | 91.6667 | 70.9677 | 60.7595 | 22 | 2 | 22 | 9 | 8 | 88.8889 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.2938 | 95.0000 | 99.7012 | 54.2527 | 2964 | 156 | 3003 | 9 | 8 | 88.8889 | |
| ltrigg-rtg1 | SNP | * | map_l100_m1_e0 | homalt | 99.8221 | 99.7445 | 99.8999 | 60.0030 | 26934 | 69 | 26933 | 27 | 24 | 88.8889 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.6259 | 94.6129 | 98.7264 | 59.9168 | 2090 | 119 | 2093 | 27 | 24 | 88.8889 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.3862 | 99.1554 | 99.6182 | 87.6455 | 2348 | 20 | 2348 | 9 | 8 | 88.8889 | |
| jmaeng-gatk | SNP | * | map_l100_m2_e0 | homalt | 84.0977 | 72.5829 | 99.9550 | 67.6272 | 19977 | 7546 | 19977 | 9 | 8 | 88.8889 | |
| jmaeng-gatk | SNP | * | map_l100_m2_e1 | homalt | 84.2134 | 72.7551 | 99.9555 | 67.5514 | 20223 | 7573 | 20223 | 9 | 8 | 88.8889 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 97.2306 | 96.8831 | 97.5806 | 79.1129 | 373 | 12 | 363 | 9 | 8 | 88.8889 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 97.4490 | 99.4792 | 95.5000 | 46.5241 | 191 | 1 | 191 | 9 | 8 | 88.8889 | |
| 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_TRlt7_lt101bp_gt95identity_merged | homalt | 52.7219 | 35.8609 | 99.5087 | 32.6223 | 1835 | 3282 | 1823 | 9 | 8 | 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 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 49.8117 | 33.2739 | 99.0333 | 46.0603 | 933 | 1871 | 922 | 9 | 8 | 88.8889 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 31.2539 | 22.7545 | 49.8886 | 70.3042 | 228 | 774 | 224 | 225 | 200 | 88.8889 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 59.7518 | 76.0417 | 49.2099 | 69.9253 | 219 | 69 | 218 | 225 | 200 | 88.8889 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 86.4484 | 76.9057 | 98.6947 | 50.6089 | 1362 | 409 | 1361 | 18 | 16 | 88.8889 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 91.8804 | 85.1605 | 99.7515 | 76.4930 | 14456 | 2519 | 14453 | 36 | 32 | 88.8889 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 91.8804 | 85.1605 | 99.7515 | 76.4930 | 14456 | 2519 | 14453 | 36 | 32 | 88.8889 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 73.2187 | 58.7771 | 97.0684 | 92.5467 | 298 | 209 | 298 | 9 | 8 | 88.8889 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 85.7476 | 75.5007 | 99.2126 | 87.1486 | 1131 | 367 | 1134 | 9 | 8 | 88.8889 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 55.1982 | 38.2022 | 99.4371 | 43.8652 | 3196 | 5170 | 3180 | 18 | 16 | 88.8889 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.7030 | 98.3471 | 99.0615 | 63.1437 | 952 | 16 | 950 | 9 | 8 | 88.8889 | |
| gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.0894 | 97.2749 | 98.9176 | 66.3428 | 1642 | 46 | 1645 | 18 | 16 | 88.8889 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 88.4669 | 80.2296 | 98.5893 | 38.6538 | 629 | 155 | 629 | 9 | 8 | 88.8889 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 87.7517 | 81.7259 | 94.7368 | 67.1785 | 161 | 36 | 162 | 9 | 8 | 88.8889 | |
| gduggal-bwaplat | INDEL | I16_PLUS | HG002compoundhet | hetalt | 78.6021 | 65.0263 | 99.3421 | 43.5644 | 1361 | 732 | 1359 | 9 | 8 | 88.8889 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 58.0645 | 69.2308 | 50.0000 | 25.0000 | 9 | 4 | 9 | 9 | 8 | 88.8889 | |
| eyeh-varpipe | INDEL | I1_5 | map_l100_m0_e0 | homalt | 98.4417 | 99.0385 | 97.8520 | 84.2540 | 206 | 2 | 410 | 9 | 8 | 88.8889 | |
| eyeh-varpipe | INDEL | I6_15 | map_siren | het | 82.9333 | 77.6224 | 89.0244 | 72.7121 | 111 | 32 | 146 | 18 | 16 | 88.8889 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.2824 | 98.0398 | 98.5261 | 67.2886 | 64070 | 1281 | 63840 | 955 | 849 | 88.9005 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.2824 | 98.0398 | 98.5261 | 67.2886 | 64070 | 1281 | 63840 | 955 | 849 | 88.9005 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 35.1776 | 30.1901 | 42.1390 | 49.2400 | 397 | 918 | 394 | 541 | 481 | 88.9094 | |
| egarrison-hhga | INDEL | * | * | het | 97.8735 | 98.9564 | 96.8141 | 57.0135 | 192107 | 2026 | 193181 | 6357 | 5653 | 88.9256 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 18.3933 | 12.4471 | 35.2174 | 39.3140 | 147 | 1034 | 162 | 298 | 265 | 88.9262 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.9331 | 96.8097 | 99.0829 | 51.7183 | 30406 | 1002 | 31224 | 289 | 257 | 88.9273 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.9331 | 96.8097 | 99.0829 | 51.7183 | 30406 | 1002 | 31224 | 289 | 257 | 88.9273 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 58.3043 | 52.2088 | 66.0112 | 56.8516 | 2080 | 1904 | 2249 | 1158 | 1030 | 88.9465 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 39.4599 | 40.5405 | 38.4354 | 56.0538 | 60 | 88 | 113 | 181 | 161 | 88.9503 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 63.5897 | 56.9678 | 71.9536 | 70.5077 | 372 | 281 | 372 | 145 | 129 | 88.9655 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 68.7500 | 83.7563 | 58.3039 | 53.7582 | 165 | 32 | 165 | 118 | 105 | 88.9831 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 65.4441 | 60.5202 | 71.2401 | 29.6193 | 1047 | 683 | 1080 | 436 | 388 | 88.9908 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 92.6375 | 87.4780 | 98.4438 | 32.3935 | 5959 | 853 | 6326 | 100 | 89 | 89.0000 | |
| ndellapenna-hhga | INDEL | D1_5 | * | * | 96.9939 | 96.6915 | 97.2981 | 56.7713 | 141890 | 4855 | 141954 | 3942 | 3509 | 89.0157 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 42.6022 | 32.6316 | 61.3466 | 68.7695 | 217 | 448 | 246 | 155 | 138 | 89.0323 | |