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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
32301-32350 / 86044 show all | |||||||||||||||
| ckim-vqsr | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5025 | 99.0393 | 99.9700 | 61.7944 | 10000 | 97 | 10000 | 3 | 3 | 100.0000 | |
| dgrover-gatk | INDEL | * | func_cds | * | 99.5531 | 99.7753 | 99.3318 | 45.1100 | 444 | 1 | 446 | 3 | 1 | 33.3333 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.8893 | 100.0000 | 99.7788 | 74.1813 | 1353 | 0 | 1353 | 3 | 1 | 33.3333 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 98.2046 | 97.0093 | 99.4297 | 73.6076 | 519 | 16 | 523 | 3 | 3 | 100.0000 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 96.9072 | 100.0000 | 94.0000 | 54.5455 | 47 | 0 | 47 | 3 | 3 | 100.0000 | |
| dgrover-gatk | INDEL | * | map_l250_m1_e0 | homalt | 96.2963 | 95.4128 | 97.1963 | 95.1496 | 104 | 5 | 104 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | * | map_l250_m2_e0 | homalt | 96.4912 | 95.6522 | 97.3451 | 95.5424 | 110 | 5 | 110 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | * | map_l250_m2_e1 | homalt | 96.5217 | 95.6897 | 97.3684 | 95.6322 | 111 | 5 | 111 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.2077 | 99.0991 | 99.3166 | 75.7056 | 440 | 4 | 436 | 3 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 96.9697 | 100.0000 | 94.1176 | 87.1859 | 52 | 0 | 48 | 3 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.4903 | 97.8659 | 99.1228 | 38.1555 | 321 | 7 | 339 | 3 | 3 | 100.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.3521 | 100.0000 | 98.7124 | 71.6889 | 230 | 0 | 230 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.0583 | 99.0196 | 97.1154 | 63.8889 | 101 | 1 | 101 | 3 | 3 | 100.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | map_l125_m1_e0 | * | 92.8571 | 96.2963 | 89.6552 | 96.7885 | 26 | 1 | 26 | 3 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | map_l150_m1_e0 | * | 87.5000 | 93.3333 | 82.3529 | 97.1138 | 14 | 1 | 14 | 3 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | map_l150_m2_e0 | * | 88.8889 | 94.1176 | 84.2105 | 97.3464 | 16 | 1 | 16 | 3 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | map_l150_m2_e1 | * | 86.4865 | 88.8889 | 84.2105 | 97.3973 | 16 | 2 | 16 | 3 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.8372 | 98.8372 | 98.8372 | 63.5593 | 255 | 3 | 255 | 3 | 3 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.8120 | 99.9059 | 99.7183 | 81.3713 | 1062 | 1 | 1062 | 3 | 1 | 33.3333 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 98.1559 | 97.0803 | 99.2556 | 71.3982 | 399 | 12 | 400 | 3 | 3 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 99.1916 | 98.5934 | 99.7970 | 32.9401 | 1472 | 21 | 1475 | 3 | 3 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.8773 | 99.8283 | 99.9264 | 44.0264 | 4070 | 7 | 4073 | 3 | 1 | 33.3333 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 95.3020 | 94.6667 | 95.9459 | 64.9289 | 71 | 4 | 71 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | D1_5 | segdup | het | 99.4942 | 99.4220 | 99.5665 | 95.0932 | 688 | 4 | 689 | 3 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.2332 | 96.8504 | 97.6190 | 79.0698 | 123 | 4 | 123 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.6017 | 99.5025 | 99.7012 | 65.7688 | 1000 | 5 | 1001 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6526 | 99.6524 | 99.6528 | 63.6057 | 860 | 3 | 861 | 3 | 2 | 66.6667 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 93.8053 | 92.9825 | 94.6429 | 99.4760 | 53 | 4 | 53 | 3 | 0 | 0.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 86.1870 | 79.6610 | 93.8776 | 52.8846 | 47 | 12 | 46 | 3 | 3 | 100.0000 | |
| ckim-isaac | INDEL | I6_15 | map_siren | * | 63.4176 | 46.8852 | 97.9592 | 84.2105 | 143 | 162 | 144 | 3 | 2 | 66.6667 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.0159 | 96.1564 | 99.9488 | 52.1398 | 5854 | 234 | 5857 | 3 | 3 | 100.0000 | |
| ckim-isaac | SNP | * | map_l100_m0_e0 | homalt | 67.7175 | 51.2048 | 99.9496 | 53.7128 | 5950 | 5670 | 5950 | 3 | 3 | 100.0000 | |
| ckim-isaac | SNP | ti | map_l100_m0_e0 | homalt | 69.6665 | 53.4731 | 99.9279 | 52.0793 | 4157 | 3617 | 4157 | 3 | 3 | 100.0000 | |
| ckim-isaac | SNP | ti | map_l125_m1_e0 | homalt | 68.7652 | 52.4129 | 99.9482 | 60.3233 | 5789 | 5256 | 5789 | 3 | 3 | 100.0000 | |
| ckim-isaac | SNP | ti | map_l125_m2_e0 | homalt | 69.3312 | 53.0727 | 99.9503 | 64.5277 | 6028 | 5330 | 6028 | 3 | 3 | 100.0000 | |
| ckim-isaac | SNP | ti | map_l150_m1_e0 | homalt | 65.1458 | 48.3281 | 99.9153 | 66.1412 | 3541 | 3786 | 3541 | 3 | 3 | 100.0000 | |
| ckim-isaac | SNP | ti | map_l150_m2_e0 | homalt | 65.7563 | 49.0021 | 99.9197 | 70.0457 | 3732 | 3884 | 3732 | 3 | 3 | 100.0000 | |
| ckim-isaac | SNP | ti | map_l250_m0_e0 | * | 68.2974 | 51.9708 | 99.5804 | 93.7826 | 712 | 658 | 712 | 3 | 1 | 33.3333 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 89.8495 | 82.0513 | 99.2857 | 77.1491 | 416 | 91 | 417 | 3 | 2 | 66.6667 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.1064 | 96.3243 | 99.9558 | 58.4821 | 6761 | 258 | 6786 | 3 | 1 | 33.3333 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 96.9007 | 94.0899 | 99.8846 | 27.3413 | 2595 | 163 | 2596 | 3 | 3 | 100.0000 | |
| ckim-isaac | SNP | tv | map_l250_m0_e0 | * | 62.1185 | 45.2288 | 99.1404 | 94.1804 | 346 | 419 | 346 | 3 | 1 | 33.3333 | |
| ckim-isaac | SNP | tv | map_l250_m0_e0 | het | 63.7441 | 47.0280 | 98.8971 | 94.7702 | 269 | 303 | 269 | 3 | 1 | 33.3333 | |
| ckim-vqsr | INDEL | * | func_cds | het | 99.3103 | 100.0000 | 98.6301 | 63.5607 | 214 | 0 | 216 | 3 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.8893 | 100.0000 | 99.7788 | 74.2205 | 1353 | 0 | 1353 | 3 | 1 | 33.3333 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 92.7242 | 86.9159 | 99.3644 | 71.0961 | 465 | 70 | 469 | 3 | 3 | 100.0000 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 47.8632 | 36.3636 | 70.0000 | 84.6154 | 16 | 28 | 7 | 3 | 3 | 100.0000 | |
| gduggal-snapfb | INDEL | I6_15 | map_l125_m0_e0 | * | 71.4286 | 66.6667 | 76.9231 | 86.8687 | 10 | 5 | 10 | 3 | 2 | 66.6667 | |
| gduggal-snapfb | INDEL | I6_15 | map_l125_m1_e0 | het | 80.3653 | 73.3333 | 88.8889 | 78.9062 | 22 | 8 | 24 | 3 | 2 | 66.6667 | |
| gduggal-snapfb | INDEL | I6_15 | map_l125_m2_e0 | het | 80.3653 | 73.3333 | 88.8889 | 82.0000 | 22 | 8 | 24 | 3 | 2 | 66.6667 | |