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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
15501-15550 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 80.5197 | 68.3077 | 98.0488 | 51.2195 | 666 | 309 | 804 | 16 | 13 | 81.2500 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 83.4407 | 85.5319 | 81.4493 | 59.0504 | 1206 | 204 | 1124 | 256 | 208 | 81.2500 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 68.9655 | 73.1707 | 65.2174 | 70.5128 | 30 | 11 | 30 | 16 | 13 | 81.2500 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 73.7836 | 58.7520 | 99.1512 | 28.6930 | 4011 | 2816 | 3738 | 32 | 26 | 81.2500 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 85.2201 | 76.0243 | 96.9466 | 64.6900 | 501 | 158 | 508 | 16 | 13 | 81.2500 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 85.2201 | 76.0243 | 96.9466 | 64.6900 | 501 | 158 | 508 | 16 | 13 | 81.2500 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 93.7833 | 93.2862 | 94.2857 | 69.6641 | 264 | 19 | 264 | 16 | 13 | 81.2500 | |
| eyeh-varpipe | INDEL | * | lowcmp_AllRepeats_gt200bp_gt95identity_merged | homalt | 58.3333 | 60.0000 | 56.7568 | 97.1604 | 3 | 2 | 21 | 16 | 13 | 81.2500 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | homalt | 52.6316 | 50.0000 | 55.5556 | 97.1787 | 2 | 2 | 20 | 16 | 13 | 81.2500 | |
| eyeh-varpipe | INDEL | C6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 80.0000 | 94.8520 | 0 | 0 | 64 | 16 | 13 | 81.2500 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.2823 | 95.8333 | 98.7758 | 84.0415 | 1242 | 54 | 1291 | 16 | 13 | 81.2500 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.7867 | 95.4172 | 98.1962 | 86.7315 | 812 | 39 | 871 | 16 | 13 | 81.2500 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.7759 | 97.0213 | 96.5318 | 75.2636 | 1368 | 42 | 1336 | 48 | 39 | 81.2500 | |
| ckim-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.7780 | 99.7214 | 99.8347 | 68.2340 | 9665 | 27 | 9665 | 16 | 13 | 81.2500 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 51.7879 | 47.6190 | 56.7568 | 99.4738 | 20 | 22 | 21 | 16 | 13 | 81.2500 | |
| astatham-gatk | SNP | * | map_l150_m1_e0 | homalt | 99.3312 | 98.8113 | 99.8566 | 68.4753 | 11139 | 134 | 11139 | 16 | 13 | 81.2500 | |
| astatham-gatk | SNP | * | map_l150_m2_e0 | homalt | 99.3470 | 98.8375 | 99.8618 | 70.8404 | 11563 | 136 | 11563 | 16 | 13 | 81.2500 | |
| astatham-gatk | SNP | * | map_l150_m2_e1 | homalt | 99.3541 | 98.8501 | 99.8633 | 70.8527 | 11691 | 136 | 11691 | 16 | 13 | 81.2500 | |
| anovak-vg | INDEL | D16_PLUS | map_siren | het | 65.2174 | 57.6923 | 75.0000 | 77.5439 | 45 | 33 | 48 | 16 | 13 | 81.2500 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.3205 | 99.5404 | 97.1300 | 67.2155 | 1083 | 5 | 1083 | 32 | 26 | 81.2500 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.7394 | 96.9504 | 96.5293 | 75.1304 | 1367 | 43 | 1335 | 48 | 39 | 81.2500 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3750 | 99.1863 | 99.5644 | 51.3896 | 3657 | 30 | 3657 | 16 | 13 | 81.2500 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.5568 | 97.9679 | 99.1528 | 76.0152 | 5978 | 124 | 7490 | 64 | 52 | 81.2500 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 97.2401 | 97.2678 | 97.2125 | 76.6096 | 534 | 15 | 558 | 16 | 13 | 81.2500 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 86.3046 | 77.4770 | 97.4025 | 63.5175 | 8586 | 2496 | 8587 | 229 | 186 | 81.2227 | |
| anovak-vg | INDEL | * | * | * | 70.4960 | 69.7491 | 71.2591 | 54.1876 | 240315 | 104227 | 248606 | 100270 | 81436 | 81.2167 | |
| jli-custom | INDEL | * | * | * | 99.3675 | 99.0788 | 99.6580 | 57.6935 | 341368 | 3174 | 341213 | 1171 | 951 | 81.2126 | |
| anovak-vg | INDEL | * | segdup | * | 73.2929 | 72.4961 | 74.1075 | 94.2874 | 1853 | 703 | 1889 | 660 | 536 | 81.2121 | |
| ciseli-custom | SNP | * | map_l100_m0_e0 | homalt | 87.9778 | 87.2289 | 88.7396 | 61.6447 | 10136 | 1484 | 10103 | 1282 | 1041 | 81.2012 | |
| mlin-fermikit | INDEL | * | map_siren | * | 83.8340 | 77.0310 | 91.9549 | 78.2144 | 5708 | 1702 | 5715 | 500 | 406 | 81.2000 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 64.0892 | 66.0415 | 62.2490 | 58.2196 | 20741 | 10665 | 29849 | 18102 | 14698 | 81.1954 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 64.0892 | 66.0415 | 62.2490 | 58.2196 | 20741 | 10665 | 29849 | 18102 | 14698 | 81.1954 | |
| astatham-gatk | INDEL | * | * | * | 99.3424 | 99.2404 | 99.4446 | 59.9126 | 341925 | 2617 | 341788 | 1909 | 1550 | 81.1943 | |
| ckim-vqsr | INDEL | D1_5 | HG002complexvar | * | 99.4499 | 99.1625 | 99.7391 | 58.6120 | 32441 | 274 | 32494 | 85 | 69 | 81.1765 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.6446 | 98.9272 | 98.3637 | 73.5579 | 30153 | 327 | 29696 | 494 | 401 | 81.1741 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.6446 | 98.9272 | 98.3637 | 73.5579 | 30153 | 327 | 29696 | 494 | 401 | 81.1741 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 37.5716 | 28.2822 | 55.9480 | 46.5176 | 1788 | 4534 | 2582 | 2033 | 1650 | 81.1608 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 37.5716 | 28.2822 | 55.9480 | 46.5176 | 1788 | 4534 | 2582 | 2033 | 1650 | 81.1608 | |
| jpowers-varprowl | INDEL | I1_5 | segdup | het | 91.4882 | 95.1673 | 88.0829 | 95.5527 | 512 | 26 | 510 | 69 | 56 | 81.1594 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 40.9601 | 29.3830 | 67.5918 | 54.6739 | 1743 | 4189 | 1583 | 759 | 616 | 81.1594 | |
| ciseli-custom | SNP | ti | map_l125_m1_e0 | homalt | 88.5271 | 87.3246 | 89.7632 | 65.2408 | 9645 | 1400 | 9628 | 1098 | 891 | 81.1475 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 21.2269 | 13.6601 | 47.5862 | 87.4784 | 209 | 1321 | 207 | 228 | 185 | 81.1404 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 21.2269 | 13.6601 | 47.5862 | 87.4784 | 209 | 1321 | 207 | 228 | 185 | 81.1404 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.2768 | 95.4919 | 99.1297 | 62.3353 | 6037 | 285 | 6037 | 53 | 43 | 81.1321 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.2768 | 95.4919 | 99.1297 | 62.3353 | 6037 | 285 | 6037 | 53 | 43 | 81.1321 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.5292 | 96.8794 | 96.1816 | 74.8551 | 1366 | 44 | 1335 | 53 | 43 | 81.1321 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 92.7883 | 86.7091 | 99.7841 | 61.8573 | 24504 | 3756 | 24493 | 53 | 43 | 81.1321 | |
| gduggal-bwavard | INDEL | D6_15 | map_siren | * | 75.5000 | 73.4774 | 77.6371 | 87.1753 | 374 | 135 | 368 | 106 | 86 | 81.1321 | |
| gduggal-bwavard | INDEL | D6_15 | map_siren | het | 83.0604 | 98.2143 | 71.9577 | 88.5593 | 275 | 5 | 272 | 106 | 86 | 81.1321 | |
| qzeng-custom | SNP | tv | map_l250_m2_e0 | het | 78.8333 | 69.8969 | 90.3898 | 96.1692 | 1356 | 584 | 1345 | 143 | 116 | 81.1189 | |