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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
9551-9600 / 86044 show all | |||||||||||||||
| ghariani-varprowl | SNP | ti | map_siren | homalt | 99.5932 | 99.4435 | 99.7434 | 52.5183 | 37705 | 211 | 37706 | 97 | 56 | 57.7320 | |
| gduggal-snapplat | INDEL | D1_5 | map_siren | * | 85.8913 | 80.9294 | 91.5013 | 89.0859 | 2856 | 673 | 3273 | 304 | 56 | 18.4211 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 49.7888 | 53.3686 | 46.6591 | 94.6882 | 808 | 706 | 824 | 942 | 56 | 5.9448 | |
| gduggal-snapvard | INDEL | D1_5 | map_l150_m2_e1 | * | 86.9569 | 95.6298 | 79.7263 | 90.1392 | 744 | 34 | 932 | 237 | 56 | 23.6287 | |
| gduggal-snapvard | INDEL | D6_15 | map_l100_m1_e0 | * | 66.5172 | 61.2403 | 72.7891 | 82.3635 | 158 | 100 | 214 | 80 | 56 | 70.0000 | |
| gduggal-snapvard | INDEL | D6_15 | map_l100_m2_e1 | het | 75.7065 | 81.4815 | 70.6960 | 83.7015 | 110 | 25 | 193 | 80 | 56 | 70.0000 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 43.9926 | 38.2022 | 51.8519 | 68.8462 | 68 | 110 | 84 | 78 | 56 | 71.7949 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 58.8919 | 70.3704 | 50.6329 | 68.7129 | 57 | 24 | 80 | 78 | 56 | 71.7949 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.0096 | 95.7223 | 96.2986 | 71.4542 | 1544 | 69 | 1535 | 59 | 56 | 94.9153 | |
| rpoplin-dv42 | SNP | * | map_l250_m2_e0 | het | 98.1499 | 98.0554 | 98.2446 | 88.1117 | 5093 | 101 | 5093 | 91 | 56 | 61.5385 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 90.5469 | 89.2517 | 91.8803 | 54.0275 | 656 | 79 | 645 | 57 | 56 | 98.2456 | |
| raldana-dualsentieon | INDEL | I6_15 | * | het | 98.4817 | 97.7076 | 99.2683 | 55.4872 | 9803 | 230 | 9768 | 72 | 56 | 77.7778 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.2981 | 93.8152 | 98.9159 | 60.6845 | 5931 | 391 | 5931 | 65 | 56 | 86.1538 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.2981 | 93.8152 | 98.9159 | 60.6845 | 5931 | 391 | 5931 | 65 | 56 | 86.1538 | |
| rpoplin-dv42 | INDEL | D1_5 | * | homalt | 99.7606 | 99.6505 | 99.8710 | 59.0122 | 48755 | 171 | 48760 | 63 | 56 | 88.8889 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.7691 | 94.9258 | 98.6854 | 40.6471 | 5631 | 301 | 5630 | 75 | 56 | 74.6667 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 93.4664 | 90.7546 | 96.3452 | 62.2067 | 2189 | 223 | 2188 | 83 | 56 | 67.4699 | |
| qzeng-custom | SNP | ti | map_l125_m2_e1 | homalt | 83.4603 | 71.9759 | 99.3054 | 66.9858 | 8247 | 3211 | 8149 | 57 | 56 | 98.2456 | |
| ltrigg-rtg2 | INDEL | I1_5 | HG002compoundhet | * | 98.0840 | 96.8760 | 99.3225 | 65.2361 | 11970 | 386 | 11875 | 81 | 56 | 69.1358 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.1473 | 97.6302 | 98.6700 | 64.9578 | 15696 | 381 | 15802 | 213 | 56 | 26.2911 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.1473 | 97.6302 | 98.6700 | 64.9578 | 15696 | 381 | 15802 | 213 | 56 | 26.2911 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 85.0366 | 86.0656 | 84.0319 | 62.7232 | 420 | 68 | 421 | 80 | 56 | 70.0000 | |
| mlin-fermikit | INDEL | I1_5 | map_l100_m2_e0 | homalt | 74.8140 | 66.2900 | 85.8537 | 77.2601 | 352 | 179 | 352 | 58 | 56 | 96.5517 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 87.6642 | 98.2456 | 79.1406 | 70.0215 | 896 | 16 | 884 | 233 | 56 | 24.0343 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 77.1804 | 63.0915 | 99.3707 | 35.9250 | 8853 | 5179 | 9000 | 57 | 56 | 98.2456 | |
| dgrover-gatk | SNP | * | map_l125_m2_e0 | het | 99.1639 | 99.3212 | 99.0070 | 77.2838 | 29119 | 199 | 29113 | 292 | 56 | 19.1781 | |
| dgrover-gatk | SNP | * | map_l125_m2_e1 | het | 99.1713 | 99.3286 | 99.0144 | 77.3174 | 29441 | 199 | 29435 | 293 | 56 | 19.1126 | |
| dgrover-gatk | SNP | ti | HG002complexvar | * | 99.9530 | 99.9268 | 99.9791 | 17.5262 | 508064 | 372 | 508000 | 106 | 56 | 52.8302 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 77.4165 | 63.6080 | 98.8826 | 71.6925 | 5913 | 3383 | 5575 | 63 | 56 | 88.8889 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 93.0487 | 95.9549 | 90.3133 | 42.3771 | 1874 | 79 | 1874 | 201 | 56 | 27.8607 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.7965 | 98.4954 | 99.0994 | 71.1241 | 28280 | 432 | 28279 | 257 | 56 | 21.7899 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.7965 | 98.4954 | 99.0994 | 71.1241 | 28280 | 432 | 28279 | 257 | 56 | 21.7899 | |
| gduggal-bwafb | SNP | tv | map_l100_m2_e1 | * | 98.8936 | 99.1694 | 98.6194 | 70.5239 | 25073 | 210 | 25073 | 351 | 56 | 15.9544 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 67.9939 | 52.5579 | 96.2669 | 70.6277 | 2065 | 1864 | 2063 | 80 | 56 | 70.0000 | |
| gduggal-bwavard | INDEL | I1_5 | segdup | * | 92.2615 | 90.9348 | 93.6275 | 94.8607 | 963 | 96 | 955 | 65 | 56 | 86.1538 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 49.9696 | 38.2775 | 71.9457 | 61.2960 | 160 | 258 | 159 | 62 | 56 | 90.3226 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 79.0807 | 98.3607 | 66.1202 | 63.2530 | 120 | 2 | 121 | 62 | 56 | 90.3226 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 50.3229 | 33.8852 | 97.7333 | 47.5634 | 1617 | 3155 | 2587 | 60 | 56 | 93.3333 | |
| gduggal-bwaplat | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 92.0320 | 86.1800 | 98.7365 | 71.8190 | 15384 | 2467 | 15395 | 197 | 56 | 28.4264 | |
| jmaeng-gatk | SNP | ti | map_l100_m2_e0 | het | 92.7126 | 88.1229 | 97.8066 | 81.8391 | 26985 | 3637 | 26978 | 605 | 56 | 9.2562 | |
| jmaeng-gatk | SNP | ti | map_l100_m2_e1 | het | 92.7795 | 88.2397 | 97.8118 | 81.8240 | 27319 | 3641 | 27312 | 611 | 56 | 9.1653 | |
| jpowers-varprowl | INDEL | I1_5 | segdup | het | 91.4882 | 95.1673 | 88.0829 | 95.5527 | 512 | 26 | 510 | 69 | 56 | 81.1594 | |
| jpowers-varprowl | SNP | ti | map_l250_m2_e1 | het | 94.1266 | 94.2407 | 94.0127 | 92.2458 | 3109 | 190 | 3109 | 198 | 56 | 28.2828 | |
| ltrigg-rtg1 | INDEL | I1_5 | * | het | 99.3128 | 98.9158 | 99.7130 | 54.8506 | 78184 | 857 | 77471 | 223 | 56 | 25.1121 | |
| jli-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.6490 | 99.5246 | 99.7737 | 73.4430 | 33078 | 158 | 33071 | 75 | 56 | 74.6667 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.1054 | 98.7352 | 99.4784 | 63.8767 | 13583 | 174 | 13541 | 71 | 56 | 78.8732 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.1054 | 98.7352 | 99.4784 | 63.8767 | 13583 | 174 | 13541 | 71 | 56 | 78.8732 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.7078 | 96.2897 | 99.1684 | 59.0884 | 8097 | 312 | 8109 | 68 | 56 | 82.3529 | |
| ckim-dragen | SNP | * | map_l125_m0_e0 | * | 98.0759 | 98.7207 | 97.4394 | 76.5498 | 19137 | 248 | 19141 | 503 | 56 | 11.1332 | |
| cchapple-custom | SNP | tv | map_l125_m0_e0 | * | 95.8633 | 96.5164 | 95.2189 | 78.5014 | 6400 | 231 | 6393 | 321 | 56 | 17.4455 | |