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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
8751-8800 / 86044 show all | |||||||||||||||
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 85.4215 | 78.1353 | 94.2062 | 35.5484 | 6386 | 1787 | 2065 | 127 | 67 | 52.7559 | |
| rpoplin-dv42 | SNP | ti | map_l150_m1_e0 | het | 98.9713 | 98.7874 | 99.1558 | 74.5638 | 12220 | 150 | 12216 | 104 | 67 | 64.4231 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.9120 | 98.2491 | 99.5839 | 53.4969 | 24915 | 444 | 24890 | 104 | 67 | 64.4231 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.1627 | 97.3832 | 96.9432 | 73.2443 | 6252 | 168 | 6216 | 196 | 67 | 34.1837 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.1627 | 97.3832 | 96.9432 | 73.2443 | 6252 | 168 | 6216 | 196 | 67 | 34.1837 | |
| ckim-vqsr | INDEL | I16_PLUS | * | homalt | 97.7080 | 99.6797 | 95.8128 | 71.8495 | 1556 | 5 | 1556 | 68 | 67 | 98.5294 | |
| ckim-vqsr | INDEL | I1_5 | HG002compoundhet | het | 94.8823 | 98.1176 | 91.8536 | 86.7262 | 834 | 16 | 778 | 69 | 67 | 97.1014 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002compoundhet | het | 88.8043 | 99.2593 | 80.3419 | 59.7015 | 402 | 3 | 282 | 69 | 67 | 97.1014 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.6966 | 92.5757 | 96.9171 | 59.1377 | 2232 | 179 | 2232 | 71 | 67 | 94.3662 | |
| astatham-gatk | INDEL | I16_PLUS | HG002compoundhet | homalt | 8.2192 | 100.0000 | 4.2857 | 73.3840 | 3 | 0 | 3 | 67 | 67 | 100.0000 | |
| astatham-gatk | SNP | * | * | homalt | 99.9742 | 99.9548 | 99.9936 | 17.1971 | 1179627 | 534 | 1179603 | 76 | 67 | 88.1579 | |
| astatham-gatk | SNP | * | map_siren | * | 93.7139 | 88.2540 | 99.8939 | 58.6796 | 129052 | 17176 | 129029 | 137 | 67 | 48.9051 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 91.9391 | 95.7447 | 88.4244 | 72.2445 | 585 | 26 | 550 | 72 | 67 | 93.0556 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 91.6225 | 98.8558 | 85.3755 | 48.1026 | 432 | 5 | 432 | 74 | 67 | 90.5405 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.9067 | 99.3856 | 96.4712 | 41.4606 | 1941 | 12 | 1941 | 71 | 67 | 94.3662 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 80.4071 | 98.1366 | 68.1034 | 35.1955 | 158 | 3 | 158 | 74 | 67 | 90.5405 | |
| asubramanian-gatk | SNP | ti | * | het | 99.0688 | 98.2225 | 99.9298 | 21.0842 | 1259105 | 22786 | 1259055 | 884 | 67 | 7.5792 | |
| jli-custom | SNP | * | map_l125_m1_e0 | * | 99.3178 | 99.0844 | 99.5522 | 66.7512 | 44912 | 415 | 44909 | 202 | 67 | 33.1683 | |
| jli-custom | SNP | * | map_l125_m2_e0 | * | 99.3286 | 99.1032 | 99.5549 | 68.8474 | 46304 | 419 | 46301 | 207 | 67 | 32.3671 | |
| jli-custom | SNP | * | map_l125_m2_e1 | * | 99.3354 | 99.1123 | 99.5595 | 68.9095 | 46783 | 419 | 46780 | 207 | 67 | 32.3671 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 59.7633 | 44.9960 | 88.9590 | 75.7274 | 562 | 687 | 564 | 70 | 67 | 95.7143 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 59.7633 | 44.9960 | 88.9590 | 75.7274 | 562 | 687 | 564 | 70 | 67 | 95.7143 | |
| jpowers-varprowl | INDEL | I1_5 | segdup | * | 91.1537 | 90.0850 | 92.2481 | 94.2204 | 954 | 105 | 952 | 80 | 67 | 83.7500 | |
| ckim-gatk | INDEL | I16_PLUS | * | homalt | 97.7080 | 99.6797 | 95.8128 | 71.8495 | 1556 | 5 | 1556 | 68 | 67 | 98.5294 | |
| ckim-dragen | INDEL | D6_15 | * | het | 99.2490 | 99.4651 | 99.0338 | 63.3339 | 11530 | 62 | 11480 | 112 | 67 | 59.8214 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.8754 | 99.0250 | 98.7263 | 71.7769 | 5789 | 57 | 5736 | 74 | 67 | 90.5405 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.8754 | 99.0250 | 98.7263 | 71.7769 | 5789 | 57 | 5736 | 74 | 67 | 90.5405 | |
| ckim-dragen | INDEL | I1_5 | HG002complexvar | * | 99.5809 | 99.4065 | 99.7559 | 56.6825 | 33165 | 198 | 33105 | 81 | 67 | 82.7160 | |
| ckim-dragen | SNP | * | map_l100_m0_e0 | het | 97.6312 | 98.8022 | 96.4876 | 75.1408 | 20951 | 254 | 20960 | 763 | 67 | 8.7811 | |
| ckim-dragen | SNP | ti | map_l150_m2_e0 | * | 98.2329 | 98.8933 | 97.5811 | 78.1929 | 20285 | 227 | 20292 | 503 | 67 | 13.3201 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9656 | 98.4786 | 99.4574 | 53.6403 | 10939 | 169 | 15763 | 86 | 67 | 77.9070 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.0973 | 99.5904 | 96.6483 | 30.9022 | 1945 | 8 | 1932 | 67 | 67 | 100.0000 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 89.1338 | 86.8027 | 91.5935 | 49.4610 | 638 | 97 | 730 | 67 | 66 | 98.5075 | |
| cchapple-custom | SNP | * | map_l250_m2_e1 | * | 96.1831 | 95.9309 | 96.4367 | 90.2654 | 7662 | 325 | 7659 | 283 | 66 | 23.3216 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 82.1817 | 76.4706 | 88.8147 | 52.8718 | 533 | 164 | 532 | 67 | 66 | 98.5075 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.6361 | 99.3135 | 86.8000 | 48.5597 | 434 | 3 | 434 | 66 | 66 | 100.0000 | |
| ciseli-custom | INDEL | D1_5 | map_siren | het | 83.5161 | 80.9398 | 86.2617 | 86.1336 | 1843 | 434 | 1846 | 294 | 66 | 22.4490 | |
| ciseli-custom | INDEL | I1_5 | map_l125_m0_e0 | * | 56.0912 | 49.6774 | 64.4068 | 91.5984 | 154 | 156 | 152 | 84 | 66 | 78.5714 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 67.6329 | 98.5915 | 51.4706 | 49.8155 | 70 | 1 | 70 | 66 | 66 | 100.0000 | |
| ckim-dragen | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.8639 | 99.1992 | 98.5310 | 73.4964 | 45336 | 366 | 45676 | 681 | 66 | 9.6916 | |
| ckim-dragen | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.8639 | 99.1992 | 98.5310 | 73.4964 | 45336 | 366 | 45676 | 681 | 66 | 9.6916 | |
| ckim-dragen | SNP | ti | map_l150_m1_e0 | * | 98.2015 | 98.8636 | 97.5482 | 76.3868 | 19488 | 224 | 19495 | 490 | 66 | 13.4694 | |
| ckim-gatk | INDEL | I16_PLUS | HG002compoundhet | homalt | 8.3333 | 100.0000 | 4.3478 | 72.9412 | 3 | 0 | 3 | 66 | 66 | 100.0000 | |
| ciseli-custom | SNP | * | map_l125_m0_e0 | het | 73.0283 | 66.5824 | 80.8560 | 84.3182 | 8432 | 4232 | 8426 | 1995 | 66 | 3.3083 | |
| rpoplin-dv42 | SNP | * | map_l250_m1_e0 | * | 98.2210 | 97.8538 | 98.5910 | 87.3689 | 7067 | 155 | 7067 | 101 | 66 | 65.3465 | |
| rpoplin-dv42 | SNP | ti | map_l100_m0_e0 | het | 99.0327 | 98.8486 | 99.2174 | 68.2957 | 13822 | 161 | 13819 | 109 | 66 | 60.5505 | |
| rpoplin-dv42 | INDEL | * | HG002compoundhet | hetalt | 95.8717 | 92.3153 | 99.7130 | 50.6553 | 23245 | 1935 | 23276 | 67 | 66 | 98.5075 | |
| mlin-fermikit | INDEL | I16_PLUS | HG002compoundhet | homalt | 8.3333 | 100.0000 | 4.3478 | 68.0556 | 3 | 0 | 3 | 66 | 66 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.7692 | 97.9625 | 99.5893 | 34.5018 | 24040 | 500 | 24005 | 99 | 66 | 66.6667 | |
| ltrigg-rtg2 | INDEL | I1_5 | HG002complexvar | * | 99.3818 | 99.0798 | 99.6856 | 52.9504 | 33055 | 307 | 32342 | 102 | 66 | 64.7059 | |