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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
72701-72750 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | SNP | * | map_l125_m2_e0 | het | 99.1177 | 99.2564 | 98.9794 | 75.5476 | 29100 | 218 | 29094 | 300 | 25 | 8.3333 | |
| hfeng-pmm2 | SNP | * | map_l125_m2_e1 | het | 99.1256 | 99.2645 | 98.9871 | 75.5812 | 29422 | 218 | 29416 | 301 | 25 | 8.3057 | |
| hfeng-pmm1 | INDEL | D6_15 | HG002complexvar | * | 97.1047 | 94.8887 | 99.4267 | 56.6618 | 5031 | 271 | 5029 | 29 | 25 | 86.2069 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.6991 | 97.6504 | 99.7706 | 72.0664 | 15211 | 366 | 15219 | 35 | 25 | 71.4286 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.9107 | 94.4420 | 99.5119 | 50.8251 | 6525 | 384 | 6524 | 32 | 25 | 78.1250 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.1875 | 95.5720 | 96.8111 | 79.9607 | 1295 | 60 | 1184 | 39 | 25 | 64.1026 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.8847 | 89.4650 | 98.7637 | 56.1710 | 2157 | 254 | 2157 | 27 | 25 | 92.5926 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.2106 | 99.7440 | 98.6829 | 40.0729 | 1948 | 5 | 1948 | 26 | 25 | 96.1538 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 89.6142 | 93.7888 | 85.7955 | 36.9176 | 151 | 10 | 151 | 25 | 25 | 100.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | HG002complexvar | homalt | 99.8477 | 99.8885 | 99.8069 | 52.0702 | 13433 | 15 | 13437 | 26 | 25 | 96.1538 | |
| hfeng-pmm2 | INDEL | D6_15 | HG002complexvar | * | 96.9573 | 94.6624 | 99.3663 | 56.8597 | 5019 | 283 | 5018 | 32 | 26 | 81.2500 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.5660 | 94.2153 | 99.0370 | 52.3174 | 3290 | 202 | 3291 | 32 | 26 | 81.2500 | |
| hfeng-pmm3 | SNP | * | map_l125_m1_e0 | * | 99.5551 | 99.4838 | 99.6266 | 69.4654 | 45093 | 234 | 45087 | 169 | 26 | 15.3846 | |
| hfeng-pmm3 | SNP | * | map_l125_m2_e0 | * | 99.5641 | 99.4949 | 99.6335 | 71.1339 | 46487 | 236 | 46481 | 171 | 26 | 15.2047 | |
| hfeng-pmm3 | SNP | * | map_l125_m2_e1 | * | 99.5664 | 99.4979 | 99.6351 | 71.1769 | 46965 | 237 | 46959 | 172 | 26 | 15.1163 | |
| hfeng-pmm1 | SNP | * | map_siren | homalt | 99.8994 | 99.8803 | 99.9184 | 53.4037 | 55090 | 66 | 55084 | 45 | 26 | 57.7778 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 90.8131 | 85.8283 | 96.4126 | 64.6593 | 860 | 142 | 860 | 32 | 26 | 81.2500 | |
| jlack-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9413 | 99.8121 | 98.0856 | 65.0500 | 27626 | 52 | 27616 | 539 | 26 | 4.8238 | |
| jlack-gatk | INDEL | * | map_l100_m1_e0 | * | 95.3278 | 97.9922 | 92.8044 | 87.6441 | 3514 | 72 | 3521 | 273 | 26 | 9.5238 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 95.7361 | 92.4350 | 99.2817 | 26.1684 | 4411 | 361 | 4423 | 32 | 26 | 81.2500 | |
| ndellapenna-hhga | INDEL | * | map_l100_m1_e0 | het | 97.2839 | 97.4049 | 97.1631 | 83.0935 | 2177 | 58 | 2192 | 64 | 26 | 40.6250 | |
| ndellapenna-hhga | INDEL | * | map_l100_m2_e0 | het | 97.3029 | 97.3992 | 97.2067 | 83.9816 | 2247 | 60 | 2262 | 65 | 26 | 40.0000 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 93.0643 | 93.0175 | 93.1111 | 72.1190 | 373 | 28 | 419 | 31 | 26 | 83.8710 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 82.6785 | 85.8537 | 79.7297 | 84.6367 | 176 | 29 | 177 | 45 | 26 | 57.7778 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 82.6785 | 85.8537 | 79.7297 | 84.6367 | 176 | 29 | 177 | 45 | 26 | 57.7778 | |
| ndellapenna-hhga | INDEL | I1_5 | HG002complexvar | hetalt | 96.3808 | 94.4380 | 98.4052 | 70.6127 | 1630 | 96 | 1666 | 27 | 26 | 96.2963 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 93.9563 | 93.3121 | 94.6095 | 71.5047 | 879 | 63 | 860 | 49 | 26 | 53.0612 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.9059 | 99.0898 | 98.7227 | 77.8437 | 2395 | 22 | 2396 | 31 | 26 | 83.8710 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 90.4993 | 83.4558 | 98.8412 | 37.5745 | 8742 | 1733 | 2900 | 34 | 26 | 76.4706 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 79.3402 | 78.0000 | 80.7273 | 54.0902 | 39 | 11 | 222 | 53 | 26 | 49.0566 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 77.3064 | 63.5256 | 98.7224 | 46.6579 | 1982 | 1138 | 2009 | 26 | 26 | 100.0000 | |
| mlin-fermikit | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 70.4762 | 90.2439 | 57.8125 | 92.6606 | 37 | 4 | 37 | 27 | 26 | 96.2963 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 76.2734 | 94.2029 | 64.0777 | 91.7797 | 65 | 4 | 66 | 37 | 26 | 70.2703 | |
| qzeng-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 91.7867 | 95.1821 | 88.6251 | 90.1491 | 810 | 41 | 896 | 115 | 26 | 22.6087 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 60.1129 | 67.5926 | 54.1237 | 69.5925 | 73 | 35 | 105 | 89 | 26 | 29.2135 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.2899 | 99.2769 | 99.3030 | 49.7051 | 961 | 7 | 8976 | 63 | 26 | 41.2698 | |
| ltrigg-rtg2 | INDEL | D6_15 | * | het | 99.2141 | 99.0942 | 99.3342 | 52.7094 | 11487 | 105 | 11339 | 76 | 26 | 34.2105 | |
| ltrigg-rtg2 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.4820 | 99.5452 | 99.4189 | 54.5520 | 55378 | 253 | 55428 | 324 | 26 | 8.0247 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 90.7127 | 92.2652 | 89.2116 | 81.5184 | 334 | 28 | 215 | 26 | 26 | 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 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.2132 | 98.0073 | 98.4200 | 74.3056 | 2410 | 49 | 2367 | 38 | 26 | 68.4211 | |
| ltrigg-rtg1 | SNP | * | map_l100_m2_e0 | homalt | 99.8182 | 99.7420 | 99.8945 | 62.4790 | 27452 | 71 | 27451 | 29 | 26 | 89.6552 | |
| ltrigg-rtg1 | SNP | * | map_l100_m2_e1 | homalt | 99.8200 | 99.7446 | 99.8955 | 62.4711 | 27725 | 71 | 27724 | 29 | 26 | 89.6552 | |
| ltrigg-rtg1 | SNP | ti | map_siren | homalt | 99.8522 | 99.7758 | 99.9287 | 51.0640 | 37831 | 85 | 37826 | 27 | 26 | 96.2963 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.3659 | 98.8427 | 99.8947 | 68.5558 | 30405 | 356 | 30350 | 32 | 26 | 81.2500 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.5176 | 97.3637 | 99.6992 | 42.0335 | 9270 | 251 | 9282 | 28 | 26 | 92.8571 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.3148 | 95.2850 | 99.4329 | 24.6012 | 4547 | 225 | 4559 | 26 | 26 | 100.0000 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.4597 | 95.3612 | 97.5838 | 52.4639 | 1254 | 61 | 1252 | 31 | 26 | 83.8710 | |
| jmaeng-gatk | SNP | ti | HG002complexvar | homalt | 99.3419 | 98.7072 | 99.9848 | 18.4737 | 190962 | 2501 | 190952 | 29 | 26 | 89.6552 | |
| jmaeng-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.0878 | 99.0624 | 99.1133 | 72.7315 | 30851 | 292 | 30851 | 276 | 26 | 9.4203 | |