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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
3201-3250 / 86044 show all | |||||||||||||||
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 40.5868 | 37.3203 | 44.4800 | 81.8709 | 571 | 959 | 556 | 694 | 384 | 55.3314 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 55.3143 | 76.7267 | 43.2455 | 81.7971 | 511 | 155 | 509 | 668 | 383 | 57.3353 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 55.3143 | 76.7267 | 43.2455 | 81.7971 | 511 | 155 | 509 | 668 | 383 | 57.3353 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 88.2450 | 85.0667 | 91.6700 | 56.4134 | 4973 | 873 | 4523 | 411 | 383 | 93.1873 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 88.2450 | 85.0667 | 91.6700 | 56.4134 | 4973 | 873 | 4523 | 411 | 383 | 93.1873 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.6759 | 98.9370 | 98.4161 | 73.8431 | 30156 | 324 | 29701 | 478 | 383 | 80.1255 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.6759 | 98.9370 | 98.4161 | 73.8431 | 30156 | 324 | 29701 | 478 | 383 | 80.1255 | |
| rpoplin-dv42 | INDEL | I6_15 | * | het | 96.6553 | 97.2291 | 96.0883 | 56.6301 | 9755 | 278 | 9752 | 397 | 383 | 96.4736 | |
| mlin-fermikit | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.5636 | 99.5347 | 95.6691 | 57.4517 | 10055 | 47 | 10073 | 456 | 383 | 83.9912 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 41.1230 | 32.4837 | 56.0227 | 78.9373 | 497 | 1033 | 493 | 387 | 383 | 98.9664 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 41.1230 | 32.4837 | 56.0227 | 78.9373 | 497 | 1033 | 493 | 387 | 383 | 98.9664 | |
| asubramanian-gatk | INDEL | D1_5 | * | * | 99.2637 | 98.9281 | 99.6016 | 61.0980 | 145172 | 1573 | 145253 | 581 | 383 | 65.9208 | |
| anovak-vg | INDEL | * | map_l125_m2_e0 | * | 72.8494 | 74.4991 | 71.2712 | 87.8407 | 1636 | 560 | 1682 | 678 | 383 | 56.4897 | |
| ckim-isaac | SNP | tv | HG002compoundhet | * | 85.3990 | 78.0567 | 94.2659 | 45.8825 | 6965 | 1958 | 7217 | 439 | 382 | 87.0159 | |
| gduggal-snapvard | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 73.0618 | 58.0378 | 98.5812 | 63.1306 | 17853 | 12908 | 28349 | 408 | 382 | 93.6275 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 64.6167 | 62.4637 | 66.9234 | 55.7051 | 1506 | 905 | 1564 | 773 | 382 | 49.4179 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 59.7902 | 69.7674 | 52.3096 | 34.3980 | 420 | 182 | 419 | 382 | 382 | 100.0000 | |
| gduggal-bwafb | SNP | ti | * | het | 99.7363 | 99.8649 | 99.6080 | 22.2231 | 1280165 | 1732 | 1280284 | 5038 | 382 | 7.5824 | |
| eyeh-varpipe | INDEL | I16_PLUS | * | het | 50.8662 | 38.8889 | 73.5049 | 38.7042 | 1057 | 1661 | 1057 | 381 | 381 | 100.0000 | |
| mlin-fermikit | INDEL | D6_15 | HG002complexvar | * | 90.8139 | 89.4568 | 92.2128 | 58.0463 | 4743 | 559 | 4784 | 404 | 381 | 94.3069 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 91.5350 | 93.7209 | 89.4487 | 79.3835 | 6239 | 418 | 6587 | 777 | 381 | 49.0347 | |
| anovak-vg | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 95.8647 | 96.7839 | 94.9628 | 65.9014 | 17003 | 565 | 17476 | 927 | 381 | 41.1003 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 88.9148 | 94.6211 | 83.8576 | 74.5711 | 2023 | 115 | 2026 | 390 | 381 | 97.6923 | |
| ckim-isaac | INDEL | * | * | homalt | 96.2069 | 93.1918 | 99.4236 | 48.6128 | 116650 | 8522 | 116601 | 676 | 381 | 56.3609 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.5684 | 96.5352 | 96.6016 | 59.0391 | 15491 | 556 | 15492 | 545 | 381 | 69.9083 | |
| qzeng-custom | SNP | * | HG002complexvar | homalt | 99.2256 | 98.6350 | 99.8233 | 20.2251 | 284636 | 3939 | 274538 | 486 | 380 | 78.1893 | |
| qzeng-custom | SNP | ti | map_l150_m1_e0 | * | 79.6789 | 67.7202 | 96.7669 | 86.5194 | 13349 | 6363 | 13259 | 443 | 380 | 85.7788 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 90.4279 | 98.3630 | 83.6775 | 77.1548 | 2103 | 35 | 2107 | 411 | 380 | 92.4574 | |
| rpoplin-dv42 | INDEL | D1_5 | HG002compoundhet | * | 95.7563 | 94.7855 | 96.7473 | 62.2778 | 11597 | 638 | 11600 | 390 | 380 | 97.4359 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.8288 | 98.4539 | 97.2116 | 67.2453 | 14391 | 226 | 14015 | 402 | 380 | 94.5274 | |
| jpowers-varprowl | INDEL | I1_5 | HG002complexvar | homalt | 96.2923 | 95.8879 | 96.7001 | 41.8106 | 12895 | 553 | 12835 | 438 | 379 | 86.5297 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 76.6125 | 83.7838 | 70.5720 | 29.6655 | 589 | 114 | 1024 | 427 | 379 | 88.7588 | |
| gduggal-bwafb | INDEL | I6_15 | * | het | 88.0827 | 80.5342 | 97.1926 | 38.4775 | 8080 | 1953 | 13848 | 400 | 379 | 94.7500 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 91.8514 | 93.2059 | 90.5357 | 48.9295 | 878 | 64 | 4276 | 447 | 379 | 84.7875 | |
| gduggal-snapfb | INDEL | * | HG002compoundhet | hetalt | 76.0060 | 64.4003 | 92.7141 | 74.7872 | 16216 | 8964 | 5739 | 451 | 378 | 83.8137 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 76.1074 | 78.6642 | 73.7116 | 78.2560 | 1696 | 460 | 1702 | 607 | 378 | 62.2735 | |
| gduggal-snapfb | SNP | * | map_l125_m0_e0 | het | 95.0102 | 96.1466 | 93.9004 | 73.7575 | 12176 | 488 | 12177 | 791 | 378 | 47.7876 | |
| ckim-dragen | SNP | ti | * | * | 99.8327 | 99.9538 | 99.7120 | 20.2602 | 2084547 | 964 | 2084816 | 6022 | 378 | 6.2770 | |
| ciseli-custom | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 89.4833 | 97.3914 | 82.7630 | 66.8151 | 26956 | 722 | 27013 | 5626 | 378 | 6.7188 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 83.6630 | 95.0637 | 74.7040 | 77.8987 | 1194 | 62 | 1199 | 406 | 377 | 92.8571 | |
| gduggal-snapvard | SNP | * | map_l100_m2_e1 | het | 93.3754 | 96.7973 | 90.1872 | 78.6618 | 45396 | 1502 | 44805 | 4875 | 376 | 7.7128 | |
| anovak-vg | INDEL | I1_5 | segdup | homalt | 68.8866 | 95.9831 | 53.7209 | 91.7355 | 454 | 19 | 462 | 398 | 376 | 94.4724 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.4963 | 97.0192 | 95.9791 | 41.7450 | 17641 | 542 | 17783 | 745 | 376 | 50.4698 | |
| eyeh-varpipe | INDEL | I6_15 | HG002compoundhet | het | 24.7604 | 59.6154 | 15.6250 | 55.8621 | 124 | 84 | 70 | 378 | 375 | 99.2063 | |
| gduggal-bwavard | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.0548 | 97.5889 | 96.5265 | 67.4923 | 34565 | 854 | 34181 | 1230 | 375 | 30.4878 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 76.4074 | 92.9624 | 64.8574 | 57.8355 | 568 | 43 | 705 | 382 | 375 | 98.1675 | |
| gduggal-snapplat | INDEL | I1_5 | HG002complexvar | * | 77.0714 | 71.7352 | 83.2654 | 65.6966 | 23933 | 9430 | 24301 | 4884 | 375 | 7.6781 | |
| raldana-dualsentieon | INDEL | I6_15 | * | * | 96.8613 | 95.4115 | 98.3558 | 49.7486 | 23684 | 1139 | 23689 | 396 | 375 | 94.6970 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 80.5507 | 87.9777 | 74.2800 | 74.5872 | 1105 | 151 | 1109 | 384 | 374 | 97.3958 | |
| hfeng-pmm1 | INDEL | * | * | het | 99.4245 | 99.1923 | 99.6578 | 58.3471 | 192565 | 1568 | 192194 | 660 | 374 | 56.6667 | |