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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
49551-49600 / 86044 show all | |||||||||||||||
| asubramanian-gatk | SNP | * | map_l150_m1_e0 | het | 41.8810 | 26.5117 | 99.6495 | 95.0572 | 5121 | 14195 | 5118 | 18 | 5 | 27.7778 | |
| mlin-fermikit | INDEL | D1_5 | map_l250_m0_e0 | het | 41.8605 | 27.2727 | 90.0000 | 94.5946 | 9 | 24 | 9 | 1 | 0 | 0.0000 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 41.8443 | 31.2155 | 63.4483 | 59.6100 | 113 | 249 | 92 | 53 | 49 | 92.4528 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 41.8118 | 28.3019 | 80.0000 | 60.9375 | 15 | 38 | 20 | 5 | 5 | 100.0000 | |
| mlin-fermikit | SNP | * | map_l250_m1_e0 | het | 41.8044 | 26.6036 | 97.5328 | 80.1621 | 1265 | 3490 | 1265 | 32 | 1 | 3.1250 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 41.7820 | 95.3547 | 26.7520 | 84.5618 | 2258 | 110 | 2340 | 6407 | 146 | 2.2788 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 41.7793 | 36.0397 | 49.6933 | 42.7847 | 1416 | 2513 | 1458 | 1476 | 1368 | 92.6829 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 41.7658 | 28.7500 | 76.3158 | 69.6000 | 46 | 114 | 58 | 18 | 18 | 100.0000 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 41.7638 | 36.3625 | 49.0496 | 86.4561 | 5846 | 10231 | 5987 | 6219 | 484 | 7.7826 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 41.7638 | 36.3625 | 49.0496 | 86.4561 | 5846 | 10231 | 5987 | 6219 | 484 | 7.7826 | |
| anovak-vg | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 41.7184 | 27.7293 | 84.1930 | 71.7265 | 381 | 993 | 1518 | 285 | 107 | 37.5439 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 41.7093 | 29.6774 | 70.1493 | 82.9517 | 46 | 109 | 47 | 20 | 19 | 95.0000 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 41.7062 | 26.8293 | 93.6170 | 94.3914 | 44 | 120 | 44 | 3 | 3 | 100.0000 | |
| gduggal-bwavard | SNP | ti | lowcmp_SimpleRepeat_diTR_51to200 | het | 41.6667 | 50.0000 | 35.7143 | 97.5567 | 5 | 5 | 5 | 9 | 0 | 0.0000 | |
| eyeh-varpipe | INDEL | D6_15 | map_l100_m0_e0 | hetalt | 41.6667 | 26.3158 | 100.0000 | 86.7925 | 5 | 14 | 14 | 0 | 0 | ||
| eyeh-varpipe | SNP | tv | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 41.6667 | 100.0000 | 26.3158 | 76.2500 | 6 | 0 | 5 | 14 | 4 | 28.5714 | |
| ciseli-custom | INDEL | I16_PLUS | segdup | homalt | 41.6667 | 26.3158 | 100.0000 | 94.5946 | 5 | 14 | 6 | 0 | 0 | ||
| asubramanian-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 41.6667 | 83.3333 | 27.7778 | 84.0708 | 5 | 1 | 5 | 13 | 1 | 7.6923 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 41.6309 | 53.2787 | 34.1623 | 32.5088 | 260 | 228 | 261 | 503 | 475 | 94.4334 | |
| asubramanian-gatk | SNP | ti | map_l125_m1_e0 | homalt | 41.5806 | 26.2472 | 100.0000 | 86.8829 | 2899 | 8146 | 2899 | 0 | 0 | ||
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 41.5658 | 38.7187 | 44.8649 | 39.9351 | 139 | 220 | 166 | 204 | 160 | 78.4314 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 41.5632 | 96.5217 | 26.4836 | 86.5727 | 1221 | 44 | 1254 | 3481 | 67 | 1.9247 | |
| gduggal-snapfb | INDEL | C1_5 | * | het | 41.5584 | 88.8889 | 27.1186 | 82.3353 | 8 | 1 | 16 | 43 | 3 | 6.9767 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 41.5565 | 39.2117 | 44.1996 | 50.5594 | 14862 | 23040 | 14844 | 18740 | 18573 | 99.1089 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 41.5500 | 37.4241 | 46.6984 | 73.3990 | 2220 | 3712 | 2256 | 2575 | 311 | 12.0777 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 41.5478 | 32.1377 | 58.7500 | 48.1865 | 224 | 473 | 235 | 165 | 147 | 89.0909 | |
| asubramanian-gatk | SNP | ti | map_l100_m0_e0 | homalt | 41.5410 | 26.2156 | 100.0000 | 85.1793 | 2038 | 5736 | 2038 | 0 | 0 | ||
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 41.5098 | 33.5081 | 54.5317 | 83.3700 | 1214 | 2409 | 1444 | 1204 | 29 | 2.4086 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 41.4960 | 66.6208 | 30.1322 | 55.6999 | 1451 | 727 | 1459 | 3383 | 3363 | 99.4088 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 41.4919 | 29.6496 | 69.0852 | 68.2046 | 220 | 522 | 219 | 98 | 82 | 83.6735 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 41.4656 | 31.8078 | 59.5455 | 61.4035 | 139 | 298 | 131 | 89 | 78 | 87.6404 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 41.4591 | 33.4290 | 54.5667 | 44.1830 | 233 | 464 | 233 | 194 | 191 | 98.4536 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 41.4578 | 77.0718 | 28.3552 | 59.9110 | 279 | 83 | 281 | 710 | 706 | 99.4366 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 41.4402 | 94.0217 | 26.5770 | 81.1312 | 1038 | 66 | 1087 | 3003 | 81 | 2.6973 | |
| gduggal-snapplat | INDEL | I6_15 | * | * | 41.4207 | 29.2310 | 71.0492 | 57.1777 | 7256 | 17567 | 7117 | 2900 | 649 | 22.3793 | |
| ckim-vqsr | SNP | ti | map_l150_m2_e1 | homalt | 41.3935 | 26.1017 | 99.9502 | 90.5160 | 2008 | 5685 | 2008 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | map_l250_m2_e0 | * | 41.3793 | 27.2727 | 85.7143 | 97.7346 | 6 | 16 | 6 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | map_l250_m2_e1 | * | 41.3793 | 27.2727 | 85.7143 | 97.7848 | 6 | 16 | 6 | 1 | 1 | 100.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | map_l150_m2_e0 | * | 41.3793 | 27.2727 | 85.7143 | 78.7879 | 3 | 8 | 6 | 1 | 1 | 100.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | map_l150_m2_e1 | * | 41.3793 | 27.2727 | 85.7143 | 79.4118 | 3 | 8 | 6 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 41.3724 | 88.2160 | 27.0230 | 51.3251 | 539 | 72 | 541 | 1461 | 1457 | 99.7262 | |
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 41.3700 | 79.5535 | 27.9532 | 77.8018 | 677 | 174 | 717 | 1848 | 48 | 2.5974 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 41.3223 | 100.0000 | 26.0417 | 79.7040 | 23 | 0 | 25 | 71 | 0 | 0.0000 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 41.2863 | 29.3252 | 69.7259 | 75.3742 | 578 | 1393 | 585 | 254 | 203 | 79.9213 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 41.2863 | 29.3252 | 69.7259 | 75.3742 | 578 | 1393 | 585 | 254 | 203 | 79.9213 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 41.2281 | 82.4561 | 27.4854 | 98.2013 | 47 | 10 | 47 | 124 | 2 | 1.6129 | |
| ckim-vqsr | SNP | ti | map_l150_m2_e0 | homalt | 41.2133 | 25.9585 | 99.9494 | 90.5585 | 1977 | 5639 | 1977 | 1 | 1 | 100.0000 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 41.2069 | 31.2292 | 60.5536 | 61.3636 | 188 | 414 | 175 | 114 | 98 | 85.9649 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 41.1854 | 27.9851 | 77.9570 | 49.7297 | 150 | 386 | 145 | 41 | 41 | 100.0000 | |
| ckim-isaac | INDEL | I6_15 | map_l150_m2_e1 | * | 41.1765 | 25.9259 | 100.0000 | 97.8723 | 7 | 20 | 7 | 0 | 0 | ||