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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16801-16850 / 86044 show all | |||||||||||||||
| ciseli-custom | SNP | ti | map_siren | homalt | 93.8892 | 94.2504 | 93.5307 | 51.3255 | 35736 | 2180 | 35566 | 2460 | 1879 | 76.3821 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 88.4938 | 92.1283 | 85.1351 | 58.7514 | 316 | 27 | 315 | 55 | 42 | 76.3636 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 86.8762 | 81.9779 | 92.3970 | 60.2527 | 3266 | 718 | 3342 | 275 | 210 | 76.3636 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.7526 | 96.6010 | 98.9320 | 70.8092 | 29444 | 1036 | 28994 | 313 | 239 | 76.3578 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.7526 | 96.6010 | 98.9320 | 70.8092 | 29444 | 1036 | 28994 | 313 | 239 | 76.3578 | |
| anovak-vg | SNP | tv | * | homalt | 99.0679 | 98.8237 | 99.3132 | 19.4559 | 372687 | 4436 | 371341 | 2568 | 1960 | 76.3240 | |
| eyeh-varpipe | INDEL | D6_15 | map_siren | * | 81.9080 | 78.5855 | 85.5238 | 80.3591 | 400 | 109 | 449 | 76 | 58 | 76.3158 | |
| eyeh-varpipe | INDEL | I1_5 | map_l100_m1_e0 | * | 96.2856 | 96.1165 | 96.4552 | 81.4147 | 1287 | 52 | 2068 | 76 | 58 | 76.3158 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.2066 | 99.0882 | 99.3253 | 55.9755 | 11193 | 103 | 11189 | 76 | 58 | 76.3158 | |
| mlin-fermikit | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.6638 | 99.3464 | 94.1222 | 70.3644 | 1216 | 8 | 1217 | 76 | 58 | 76.3158 | |
| ghariani-varprowl | INDEL | * | func_cds | het | 90.6725 | 97.6636 | 84.6154 | 54.4280 | 209 | 5 | 209 | 38 | 29 | 76.3158 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.7125 | 97.6953 | 99.7510 | 72.1894 | 15218 | 359 | 15225 | 38 | 29 | 76.3158 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.3978 | 94.1426 | 96.6870 | 72.1399 | 1109 | 69 | 1109 | 38 | 29 | 76.3158 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 80.5518 | 94.6809 | 70.0921 | 54.5132 | 445 | 25 | 989 | 422 | 322 | 76.3033 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.4308 | 99.2074 | 99.6552 | 61.9169 | 28036 | 224 | 28038 | 97 | 74 | 76.2887 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 51.0807 | 34.9679 | 94.7321 | 49.3900 | 1091 | 2029 | 1061 | 59 | 45 | 76.2712 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9205 | 98.2346 | 99.6161 | 72.9579 | 15302 | 275 | 15309 | 59 | 45 | 76.2712 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.9986 | 97.0872 | 98.9273 | 73.5231 | 6233 | 187 | 7378 | 80 | 61 | 76.2500 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.9986 | 97.0872 | 98.9273 | 73.5231 | 6233 | 187 | 7378 | 80 | 61 | 76.2500 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 40.5494 | 35.4887 | 47.2934 | 60.0683 | 236 | 429 | 332 | 370 | 282 | 76.2162 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 97.3524 | 99.2470 | 95.5288 | 54.1878 | 8303 | 63 | 8888 | 416 | 317 | 76.2019 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8817 | 99.8462 | 99.9171 | 55.0271 | 25320 | 39 | 25323 | 21 | 16 | 76.1905 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8718 | 99.8265 | 99.9171 | 55.1617 | 25315 | 44 | 25318 | 21 | 16 | 76.1905 | |
| dgrover-gatk | SNP | * | map_l100_m1_e0 | homalt | 99.7105 | 99.5001 | 99.9219 | 58.2002 | 26868 | 135 | 26868 | 21 | 16 | 76.1905 | |
| dgrover-gatk | SNP | * | map_l100_m2_e0 | homalt | 99.7105 | 99.4986 | 99.9234 | 60.6643 | 27385 | 138 | 27385 | 21 | 16 | 76.1905 | |
| dgrover-gatk | SNP | * | map_l100_m2_e1 | homalt | 99.7116 | 99.4999 | 99.9241 | 60.6444 | 27657 | 139 | 27657 | 21 | 16 | 76.1905 | |
| ckim-vqsr | SNP | * | HG002compoundhet | * | 98.9056 | 97.9940 | 99.8343 | 41.9777 | 25304 | 518 | 25301 | 42 | 32 | 76.1905 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 73.1041 | 58.3425 | 97.8659 | 40.1460 | 1063 | 759 | 963 | 21 | 16 | 76.1905 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 89.2143 | 91.5033 | 87.0370 | 76.6234 | 140 | 13 | 141 | 21 | 16 | 76.1905 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 93.1711 | 99.1342 | 87.8846 | 63.1467 | 458 | 4 | 457 | 63 | 48 | 76.1905 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.4217 | 95.9190 | 98.9723 | 59.1578 | 6064 | 258 | 6067 | 63 | 48 | 76.1905 | |
| jli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.4217 | 95.9190 | 98.9723 | 59.1578 | 6064 | 258 | 6067 | 63 | 48 | 76.1905 | |
| ltrigg-rtg1 | INDEL | D6_15 | HG002complexvar | * | 97.6527 | 96.5862 | 98.7430 | 52.4974 | 5121 | 181 | 4949 | 63 | 48 | 76.1905 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.8130 | 98.1907 | 99.4431 | 58.6332 | 3799 | 70 | 3750 | 21 | 16 | 76.1905 | |
| gduggal-bwavard | SNP | * | map_l100_m0_e0 | homalt | 98.4857 | 97.1945 | 99.8116 | 63.6530 | 11294 | 326 | 11127 | 21 | 16 | 76.1905 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 70.3015 | 64.9123 | 76.6667 | 98.8432 | 37 | 20 | 69 | 21 | 16 | 76.1905 | |
| hfeng-pmm1 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.1710 | 92.9950 | 95.3770 | 77.2463 | 3757 | 283 | 3466 | 168 | 128 | 76.1905 | |
| gduggal-snapvard | SNP | * | map_l150_m0_e0 | homalt | 96.6127 | 93.9349 | 99.4477 | 77.1281 | 3841 | 248 | 3781 | 21 | 16 | 76.1905 | |
| jlack-gatk | SNP | * | map_l100_m0_e0 | homalt | 98.9979 | 98.1928 | 99.8163 | 60.9544 | 11410 | 210 | 11410 | 21 | 16 | 76.1905 | |
| ciseli-custom | INDEL | D16_PLUS | map_siren | homalt | 60.7595 | 70.5882 | 53.3333 | 89.9103 | 24 | 10 | 24 | 21 | 16 | 76.1905 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 26.6490 | 16.9856 | 61.8182 | 56.0000 | 71 | 347 | 68 | 42 | 32 | 76.1905 | |
| ckim-dragen | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 97.2860 | 97.0041 | 97.5694 | 83.2558 | 939 | 29 | 843 | 21 | 16 | 76.1905 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.5026 | 97.4692 | 99.5582 | 62.4506 | 1502 | 39 | 4732 | 21 | 16 | 76.1905 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 81.9633 | 76.1261 | 88.7701 | 48.1994 | 169 | 53 | 166 | 21 | 16 | 76.1905 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 69.2913 | 80.0000 | 61.1111 | 70.0000 | 40 | 10 | 33 | 21 | 16 | 76.1905 | |
| dgrover-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.4181 | 99.5505 | 99.2861 | 75.9770 | 48054 | 217 | 47844 | 344 | 262 | 76.1628 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 89.9267 | 99.0645 | 82.3323 | 76.8153 | 2118 | 20 | 2111 | 453 | 345 | 76.1589 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.7589 | 96.5419 | 99.0070 | 60.1541 | 15215 | 545 | 15055 | 151 | 115 | 76.1589 | |
| qzeng-custom | INDEL | D1_5 | HG002compoundhet | * | 88.1713 | 85.4271 | 91.0977 | 64.3947 | 10452 | 1783 | 11502 | 1124 | 856 | 76.1566 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 68.5075 | 66.4183 | 70.7325 | 47.6018 | 13192 | 6670 | 15431 | 6385 | 4862 | 76.1472 | |