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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
60801-60850 / 86044 show all | |||||||||||||||
| ltrigg-rtg2 | INDEL | I1_5 | tech_badpromoters | het | 94.1176 | 100.0000 | 88.8889 | 43.7500 | 8 | 0 | 8 | 1 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | D1_5 | tech_badpromoters | homalt | 100.0000 | 100.0000 | 100.0000 | 43.7500 | 9 | 0 | 9 | 0 | 0 | ||
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 78.1733 | 64.2951 | 99.6920 | 43.7482 | 3904 | 2168 | 3884 | 12 | 10 | 83.3333 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.9067 | 99.8135 | 100.0000 | 43.7478 | 1606 | 3 | 1606 | 0 | 0 | ||
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 79.5102 | 66.0798 | 99.7928 | 43.7451 | 1276 | 655 | 1445 | 3 | 2 | 66.6667 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 79.5102 | 66.0798 | 99.7928 | 43.7451 | 1276 | 655 | 1445 | 3 | 2 | 66.6667 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 79.6213 | 77.5816 | 81.7711 | 43.7436 | 3163 | 914 | 3158 | 704 | 666 | 94.6023 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.7813 | 99.6999 | 99.8628 | 43.7307 | 3655 | 11 | 3639 | 5 | 5 | 100.0000 | |
| gduggal-bwafb | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.2813 | 99.8597 | 98.7097 | 43.7241 | 2135 | 3 | 2142 | 28 | 3 | 10.7143 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 26.5368 | 18.6688 | 45.8678 | 43.7209 | 115 | 501 | 111 | 131 | 110 | 83.9695 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 64.4666 | 47.9448 | 98.3624 | 43.7187 | 3266 | 3546 | 2763 | 46 | 36 | 78.2609 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 9.3220 | 7.7465 | 11.7021 | 43.7126 | 11 | 131 | 11 | 83 | 83 | 100.0000 | |
| gduggal-snapvard | INDEL | I16_PLUS | * | homalt | 1.5180 | 0.7687 | 60.0000 | 43.7086 | 12 | 1549 | 51 | 34 | 22 | 64.7059 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.4824 | 95.5531 | 99.4912 | 43.7067 | 13172 | 613 | 13100 | 67 | 62 | 92.5373 | |
| jpowers-varprowl | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 98.2022 | 100.0000 | 96.4680 | 43.7034 | 1311 | 0 | 1311 | 48 | 32 | 66.6667 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.0999 | 94.4231 | 99.9328 | 43.7027 | 2946 | 174 | 2975 | 2 | 2 | 100.0000 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.4728 | 99.0810 | 99.8678 | 43.7004 | 2264 | 21 | 2267 | 3 | 0 | 0.0000 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0614 | 99.8136 | 98.3203 | 43.6922 | 10712 | 20 | 10712 | 183 | 5 | 2.7322 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8445 | 99.7514 | 99.9377 | 43.6886 | 1605 | 4 | 1605 | 1 | 1 | 100.0000 | |
| ciseli-custom | INDEL | * | func_cds | het | 79.1762 | 80.8411 | 77.5785 | 43.6869 | 173 | 41 | 173 | 50 | 20 | 40.0000 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 80.7791 | 74.7144 | 87.9154 | 43.6787 | 10921 | 3696 | 21956 | 3018 | 1053 | 34.8907 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 50.4626 | 34.9887 | 90.4762 | 43.6782 | 155 | 288 | 133 | 14 | 11 | 78.5714 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.5655 | 97.5492 | 99.6032 | 43.6746 | 2229 | 56 | 2510 | 10 | 3 | 30.0000 | |
| anovak-vg | SNP | * | HG002compoundhet | * | 78.0620 | 76.6207 | 79.5586 | 43.6697 | 19785 | 6037 | 20297 | 5215 | 3696 | 70.8725 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.8650 | 99.8038 | 99.9264 | 43.6688 | 4069 | 8 | 4072 | 3 | 1 | 33.3333 | |
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.0377 | 88.9807 | 99.7041 | 43.6667 | 323 | 40 | 337 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.0377 | 88.9807 | 99.7041 | 43.6667 | 323 | 40 | 337 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 67.3819 | 51.3536 | 97.9554 | 43.6649 | 607 | 575 | 527 | 11 | 5 | 45.4545 | |
| ltrigg-rtg1 | INDEL | * | tech_badpromoters | het | 98.7342 | 100.0000 | 97.5000 | 43.6620 | 39 | 0 | 39 | 1 | 0 | 0.0000 | |
| ckim-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.2863 | 99.7441 | 96.8705 | 43.6595 | 4677 | 12 | 4674 | 151 | 1 | 0.6623 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.3623 | 98.8621 | 99.8675 | 43.6567 | 2259 | 26 | 2262 | 3 | 0 | 0.0000 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 60.5607 | 55.5947 | 66.5009 | 43.6531 | 6161 | 4921 | 6019 | 3032 | 2878 | 94.9208 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.9091 | 95.9594 | 97.8778 | 43.6515 | 13228 | 557 | 14482 | 314 | 297 | 94.5860 | |
| ltrigg-rtg1 | INDEL | I6_15 | * | homalt | 98.7666 | 98.4933 | 99.0414 | 43.6510 | 6145 | 94 | 6096 | 59 | 52 | 88.1356 | |
| mlin-fermikit | SNP | tv | tech_badpromoters | * | 93.7063 | 93.0556 | 94.3662 | 43.6508 | 67 | 5 | 67 | 4 | 2 | 50.0000 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 68.3658 | 51.9362 | 100.0000 | 43.6433 | 228 | 211 | 297 | 0 | 0 | ||
| ndellapenna-hhga | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8164 | 99.7288 | 99.9041 | 43.6419 | 6251 | 17 | 6252 | 6 | 5 | 83.3333 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 28.9696 | 23.8776 | 36.8222 | 43.6389 | 117 | 373 | 292 | 501 | 425 | 84.8303 | |
| ndellapenna-hhga | INDEL | D6_15 | * | hetalt | 65.7378 | 49.3394 | 98.4629 | 43.6387 | 4033 | 4141 | 3459 | 54 | 41 | 75.9259 | |
| gduggal-snapvard | INDEL | I6_15 | func_cds | het | 69.8061 | 87.5000 | 58.0645 | 43.6364 | 21 | 3 | 18 | 13 | 12 | 92.3077 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.9176 | 98.2314 | 99.6135 | 43.6336 | 10886 | 196 | 10826 | 42 | 39 | 92.8571 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 88.8331 | 79.9097 | 100.0000 | 43.6306 | 354 | 89 | 354 | 0 | 0 | ||
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.6606 | 99.5951 | 97.7434 | 43.6301 | 5658 | 23 | 5631 | 130 | 122 | 93.8462 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 91.6463 | 96.0573 | 87.6226 | 43.6282 | 1876 | 77 | 1876 | 265 | 94 | 35.4717 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 57.8592 | 55.4482 | 60.4894 | 43.6279 | 17739 | 14253 | 30010 | 19602 | 17898 | 91.3070 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.7362 | 97.5039 | 100.0000 | 43.6266 | 625 | 16 | 628 | 0 | 0 | ||
| gduggal-snapvard | INDEL | * | func_cds | * | 83.0794 | 82.2472 | 83.9286 | 43.6242 | 366 | 79 | 423 | 81 | 65 | 80.2469 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.4894 | 95.1923 | 99.9000 | 43.6220 | 2970 | 150 | 2998 | 3 | 3 | 100.0000 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 70.2794 | 91.7657 | 56.9459 | 43.6183 | 1081 | 97 | 3718 | 2811 | 2776 | 98.7549 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.8452 | 98.0861 | 99.6161 | 43.6147 | 410 | 8 | 519 | 2 | 1 | 50.0000 | |