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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16601-16650 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.1543 | 98.3354 | 97.9739 | 68.1869 | 13528 | 229 | 13491 | 279 | 216 | 77.4194 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.1543 | 98.3354 | 97.9739 | 68.1869 | 13528 | 229 | 13491 | 279 | 216 | 77.4194 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.1965 | 97.0144 | 99.4078 | 64.7466 | 15597 | 480 | 15611 | 93 | 72 | 77.4194 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.1965 | 97.0144 | 99.4078 | 64.7466 | 15597 | 480 | 15611 | 93 | 72 | 77.4194 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 57.9193 | 56.2153 | 59.7299 | 62.4801 | 36735 | 28612 | 56563 | 38135 | 29523 | 77.4171 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 57.9193 | 56.2153 | 59.7299 | 62.4801 | 36735 | 28612 | 56563 | 38135 | 29523 | 77.4171 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 54.1762 | 50.3884 | 58.5798 | 35.8416 | 10378 | 10218 | 11153 | 7886 | 6105 | 77.4157 | |
| gduggal-snapvard | INDEL | I1_5 | * | het | 89.2130 | 96.8839 | 82.6678 | 61.9450 | 76578 | 2463 | 82223 | 17239 | 13345 | 77.4117 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.1021 | 99.2658 | 98.9390 | 69.0925 | 13656 | 101 | 13614 | 146 | 113 | 77.3973 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.1021 | 99.2658 | 98.9390 | 69.0925 | 13656 | 101 | 13614 | 146 | 113 | 77.3973 | |
| gduggal-bwaplat | INDEL | D16_PLUS | * | * | 82.9287 | 71.7129 | 98.3034 | 72.8727 | 4865 | 1919 | 4867 | 84 | 65 | 77.3810 | |
| qzeng-custom | INDEL | * | * | hetalt | 86.3714 | 76.5503 | 99.0835 | 60.3958 | 19319 | 5918 | 5730 | 53 | 41 | 77.3585 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 82.8053 | 79.1762 | 86.7830 | 47.8544 | 346 | 91 | 348 | 53 | 41 | 77.3585 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 88.3380 | 89.7756 | 86.9458 | 76.1737 | 360 | 41 | 353 | 53 | 41 | 77.3585 | |
| qzeng-custom | SNP | * | map_l100_m2_e1 | het | 87.9932 | 79.9949 | 97.7685 | 81.4422 | 37516 | 9382 | 37154 | 848 | 656 | 77.3585 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 92.1428 | 89.6098 | 94.8232 | 41.9297 | 32790 | 3802 | 32348 | 1766 | 1366 | 77.3499 | |
| ciseli-custom | INDEL | I1_5 | HG002complexvar | * | 86.2012 | 84.5873 | 87.8779 | 52.9140 | 28220 | 5142 | 27874 | 3845 | 2974 | 77.3472 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 66.4735 | 78.6403 | 57.5670 | 62.2369 | 23968 | 6510 | 51344 | 37846 | 29268 | 77.3345 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 66.4735 | 78.6403 | 57.5670 | 62.2369 | 23968 | 6510 | 51344 | 37846 | 29268 | 77.3345 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.9439 | 96.7636 | 99.1534 | 64.2879 | 63236 | 2115 | 63011 | 538 | 416 | 77.3234 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.9439 | 96.7636 | 99.1534 | 64.2879 | 63236 | 2115 | 63011 | 538 | 416 | 77.3234 | |
| ghariani-varprowl | INDEL | D6_15 | HG002complexvar | homalt | 83.9832 | 79.7263 | 88.7204 | 58.7246 | 932 | 237 | 936 | 119 | 92 | 77.3109 | |
| eyeh-varpipe | INDEL | I1_5 | map_siren | * | 96.0860 | 95.6406 | 96.5357 | 78.7530 | 2874 | 131 | 3316 | 119 | 92 | 77.3109 | |
| anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 27.3104 | 23.7037 | 32.2115 | 41.0765 | 32 | 103 | 67 | 141 | 109 | 77.3050 | |
| gduggal-bwavard | SNP | * | * | homalt | 99.5128 | 99.0597 | 99.9700 | 16.7717 | 1169065 | 11097 | 1159771 | 348 | 269 | 77.2989 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 18.8114 | 10.6154 | 82.5397 | 71.8121 | 69 | 581 | 104 | 22 | 17 | 77.2727 | |
| gduggal-bwafb | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5732 | 99.3661 | 99.7812 | 63.9280 | 10033 | 64 | 10032 | 22 | 17 | 77.2727 | |
| gduggal-bwaplat | INDEL | I6_15 | HG002complexvar | homalt | 91.5364 | 85.9143 | 97.9458 | 60.0075 | 1043 | 171 | 1049 | 22 | 17 | 77.2727 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.0919 | 98.8333 | 99.3518 | 73.8158 | 2965 | 35 | 3372 | 22 | 17 | 77.2727 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 98.4133 | 98.4093 | 98.4173 | 55.0598 | 1361 | 22 | 1368 | 22 | 17 | 77.2727 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 26.5124 | 15.4269 | 94.2105 | 53.3742 | 365 | 2001 | 358 | 22 | 17 | 77.2727 | |
| ghariani-varprowl | INDEL | * | segdup | homalt | 93.7217 | 90.2083 | 97.5197 | 91.8211 | 866 | 94 | 865 | 22 | 17 | 77.2727 | |
| hfeng-pmm3 | INDEL | D6_15 | HG002complexvar | het | 95.8678 | 92.7244 | 99.2318 | 57.2218 | 2893 | 227 | 2842 | 22 | 17 | 77.2727 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.4263 | 99.4533 | 99.3994 | 51.5732 | 3638 | 20 | 3641 | 22 | 17 | 77.2727 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.5329 | 95.0920 | 98.0180 | 79.6517 | 1085 | 56 | 1088 | 22 | 17 | 77.2727 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.4449 | 95.8541 | 99.0894 | 62.1020 | 2312 | 100 | 2394 | 22 | 17 | 77.2727 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 90.8242 | 84.7922 | 97.7800 | 34.6306 | 959 | 172 | 969 | 22 | 17 | 77.2727 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 56.8514 | 55.5879 | 58.1738 | 61.2449 | 24089 | 19246 | 24394 | 17539 | 13551 | 77.2621 | |
| anovak-vg | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 65.3950 | 71.2167 | 60.4531 | 49.7479 | 3986 | 1611 | 5844 | 3823 | 2953 | 77.2430 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 21.0208 | 18.3844 | 24.5399 | 66.7686 | 66 | 293 | 80 | 246 | 190 | 77.2358 | |
| ckim-gatk | INDEL | D6_15 | * | het | 98.7882 | 99.4997 | 98.0868 | 64.1200 | 11534 | 58 | 11484 | 224 | 173 | 77.2321 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 71.3186 | 75.9474 | 67.2215 | 47.6957 | 9018 | 2856 | 12237 | 5967 | 4608 | 77.2247 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 61.2290 | 64.8241 | 58.0117 | 44.0961 | 11551 | 6268 | 20937 | 15154 | 11698 | 77.1941 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 49.4570 | 43.9271 | 56.5797 | 43.4855 | 4868 | 6214 | 5009 | 3844 | 2967 | 77.1852 | |
| asubramanian-gatk | INDEL | * | * | homalt | 99.2686 | 99.5207 | 99.0178 | 58.9491 | 124572 | 600 | 124599 | 1236 | 954 | 77.1845 | |
| gduggal-snapvard | INDEL | I6_15 | map_l150_m1_e0 | * | 60.8583 | 72.0000 | 52.7027 | 87.7888 | 18 | 7 | 39 | 35 | 27 | 77.1429 | |
| gduggal-snapvard | INDEL | I6_15 | map_l150_m1_e0 | het | 63.8563 | 93.3333 | 48.5294 | 87.8571 | 14 | 1 | 33 | 35 | 27 | 77.1429 | |
| gduggal-snapvard | SNP | * | map_l125_m1_e0 | homalt | 97.9102 | 96.1077 | 99.7817 | 66.1808 | 16247 | 658 | 15999 | 35 | 27 | 77.1429 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 39.2362 | 37.2842 | 41.4038 | 61.8887 | 2268 | 3815 | 2336 | 3306 | 2550 | 77.1325 | |
| mlin-fermikit | INDEL | * | map_l100_m2_e1 | * | 75.3445 | 66.1342 | 87.5352 | 80.6829 | 2484 | 1272 | 2486 | 354 | 273 | 77.1186 | |