PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
63551-63600 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | D1_5 | * | homalt | 99.7928 | 99.9285 | 99.6576 | 62.5365 | 48891 | 35 | 48898 | 168 | 166 | 98.8095 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 96.1967 | 95.2767 | 97.1347 | 75.0892 | 706 | 35 | 678 | 20 | 18 | 90.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 93.9805 | 88.9241 | 99.6466 | 70.0529 | 281 | 35 | 282 | 1 | 1 | 100.0000 | |
| jpowers-varprowl | INDEL | * | map_l250_m1_e0 | * | 90.7563 | 88.5246 | 93.1034 | 96.3179 | 270 | 35 | 270 | 20 | 12 | 60.0000 | |
| jpowers-varprowl | INDEL | * | map_l250_m2_e0 | * | 91.3580 | 89.4260 | 93.3754 | 96.4605 | 296 | 35 | 296 | 21 | 12 | 57.1429 | |
| jpowers-varprowl | INDEL | * | map_l250_m2_e1 | * | 91.4110 | 89.4895 | 93.4169 | 96.5296 | 298 | 35 | 298 | 21 | 12 | 57.1429 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 37.1767 | 79.2899 | 24.2806 | 53.7438 | 134 | 35 | 135 | 421 | 420 | 99.7625 | |
| jli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 95.1908 | 91.4842 | 99.2105 | 70.2428 | 376 | 35 | 377 | 3 | 3 | 100.0000 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.8004 | 97.8301 | 97.7707 | 70.7090 | 1578 | 35 | 1535 | 35 | 26 | 74.2857 | |
| jli-custom | INDEL | I1_5 | map_siren | * | 99.2153 | 98.8353 | 99.5983 | 78.8156 | 2970 | 35 | 2975 | 12 | 4 | 33.3333 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.3359 | 95.5357 | 99.2053 | 39.4061 | 749 | 35 | 749 | 6 | 6 | 100.0000 | |
| jpowers-varprowl | INDEL | I16_PLUS | HG002compoundhet | het | 3.5500 | 25.5319 | 1.9076 | 52.7962 | 12 | 35 | 19 | 977 | 973 | 99.5906 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 35 | 0 | 0 | 0 | |||
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 79.9744 | 90.9326 | 71.3733 | 92.8433 | 351 | 35 | 369 | 148 | 33 | 22.2973 | |
| jpowers-varprowl | SNP | tv | func_cds | * | 98.8262 | 99.1993 | 98.4559 | 36.2571 | 4336 | 35 | 4336 | 68 | 5 | 7.3529 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 89.9659 | 85.8300 | 94.5205 | 76.9716 | 212 | 35 | 207 | 12 | 8 | 66.6667 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 94.0938 | 92.8279 | 95.3947 | 79.6156 | 453 | 35 | 435 | 21 | 12 | 57.1429 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 88.2868 | 81.1828 | 96.7532 | 67.3729 | 151 | 35 | 149 | 5 | 4 | 80.0000 | |
| egarrison-hhga | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7968 | 99.6842 | 99.9096 | 55.6842 | 11049 | 35 | 11049 | 10 | 7 | 70.0000 | |
| egarrison-hhga | INDEL | * | map_siren | homalt | 98.7934 | 98.6817 | 98.9052 | 79.7136 | 2620 | 35 | 2620 | 29 | 20 | 68.9655 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.5379 | 95.4068 | 95.6693 | 67.9563 | 727 | 35 | 729 | 33 | 24 | 72.7273 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.1017 | 90.7652 | 93.4783 | 56.5012 | 344 | 35 | 344 | 24 | 14 | 58.3333 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 93.4647 | 97.8852 | 89.4261 | 56.5157 | 1620 | 35 | 1683 | 199 | 186 | 93.4673 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 72.8872 | 59.3023 | 94.5455 | 73.4300 | 51 | 35 | 52 | 3 | 2 | 66.6667 | |
| ckim-isaac | INDEL | I6_15 | map_l100_m1_e0 | het | 57.1133 | 40.6780 | 95.8333 | 92.5697 | 24 | 35 | 23 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | I6_15 | map_l100_m2_e0 | het | 59.0641 | 42.6230 | 96.1538 | 92.8177 | 26 | 35 | 25 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | I6_15 | map_l100_m2_e1 | het | 59.0641 | 42.6230 | 96.1538 | 92.8767 | 26 | 35 | 25 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | I6_15 | map_l125_m1_e0 | * | 50.7042 | 33.9623 | 100.0000 | 94.6903 | 18 | 35 | 18 | 0 | 0 | ||
| ckim-isaac | INDEL | I6_15 | map_l125_m2_e0 | * | 50.7042 | 33.9623 | 100.0000 | 95.3368 | 18 | 35 | 18 | 0 | 0 | ||
| ckim-isaac | INDEL | I6_15 | map_l125_m2_e1 | * | 50.7042 | 33.9623 | 100.0000 | 95.4774 | 18 | 35 | 18 | 0 | 0 | ||
| ckim-isaac | SNP | * | map_siren | hetalt | 72.4409 | 56.7901 | 100.0000 | 72.4551 | 46 | 35 | 46 | 0 | 0 | ||
| ckim-isaac | SNP | tv | map_siren | hetalt | 72.4409 | 56.7901 | 100.0000 | 72.4551 | 46 | 35 | 46 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | HG002complexvar | homalt | 99.7470 | 99.8705 | 99.6237 | 57.3434 | 26992 | 35 | 27005 | 102 | 98 | 96.0784 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.0969 | 99.4760 | 98.7206 | 57.2310 | 6644 | 35 | 6636 | 86 | 83 | 96.5116 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 94.9242 | 90.7895 | 99.4536 | 60.9392 | 345 | 35 | 364 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.5441 | 97.3505 | 99.7673 | 61.8300 | 1286 | 35 | 1286 | 3 | 2 | 66.6667 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.5591 | 99.1221 | 100.0000 | 34.4828 | 3952 | 35 | 3952 | 0 | 0 | ||
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8508 | 99.7870 | 99.9147 | 58.6642 | 16394 | 35 | 16393 | 14 | 4 | 28.5714 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9103 | 98.0469 | 97.7741 | 69.5010 | 1757 | 35 | 1757 | 40 | 30 | 75.0000 | |
| dgrover-gatk | INDEL | D6_15 | HG002complexvar | het | 99.0464 | 98.8782 | 99.2152 | 59.4430 | 3085 | 35 | 3034 | 24 | 18 | 75.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.6403 | 99.3747 | 97.9167 | 72.3397 | 5562 | 35 | 5546 | 118 | 106 | 89.8305 | |
| dgrover-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 99.0037 | 98.8395 | 99.1683 | 69.7220 | 2981 | 35 | 2981 | 25 | 8 | 32.0000 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 91.0387 | 84.9785 | 98.0296 | 74.3687 | 198 | 35 | 199 | 4 | 3 | 75.0000 | |
| egarrison-hhga | INDEL | * | map_l100_m1_e0 | hetalt | 82.7545 | 71.7742 | 97.7011 | 88.8031 | 89 | 35 | 85 | 2 | 1 | 50.0000 | |
| egarrison-hhga | INDEL | * | map_l100_m2_e0 | hetalt | 82.9138 | 72.0000 | 97.7273 | 89.6104 | 90 | 35 | 86 | 2 | 1 | 50.0000 | |
| egarrison-hhga | INDEL | * | map_l150_m1_e0 | * | 97.6046 | 97.3842 | 97.8261 | 98.6310 | 1303 | 35 | 1305 | 29 | 10 | 34.4828 | |
| egarrison-hhga | INDEL | * | map_l150_m2_e0 | * | 97.7239 | 97.5142 | 97.9345 | 98.6965 | 1373 | 35 | 1375 | 29 | 10 | 34.4828 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 76.3948 | 71.7742 | 81.6514 | 99.9459 | 89 | 35 | 89 | 20 | 12 | 60.0000 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 96.9502 | 96.5174 | 97.3869 | 63.5264 | 970 | 35 | 969 | 26 | 17 | 65.3846 | |
| ndellapenna-hhga | INDEL | D6_15 | map_siren | hetalt | 75.3022 | 64.6465 | 90.1639 | 76.8061 | 64 | 35 | 55 | 6 | 2 | 33.3333 | |