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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
82751-82800 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.1803 | 96.5537 | 97.8151 | 57.7486 | 17062 | 609 | 17057 | 381 | 365 | 95.8005 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 84.8128 | 90.0176 | 80.1769 | 69.3559 | 1533 | 170 | 1541 | 381 | 365 | 95.8005 | |
| jmaeng-gatk | INDEL | D6_15 | * | * | 97.9970 | 97.6008 | 98.3964 | 55.6203 | 25466 | 626 | 25465 | 415 | 366 | 88.1928 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 80.5286 | 73.7548 | 88.6726 | 69.8081 | 3687 | 1312 | 3781 | 483 | 366 | 75.7764 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 80.5286 | 73.7548 | 88.6726 | 69.8081 | 3687 | 1312 | 3781 | 483 | 366 | 75.7764 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 82.5487 | 75.1600 | 91.5487 | 63.9730 | 3994 | 1320 | 4008 | 370 | 366 | 98.9189 | |
| bgallagher-sentieon | INDEL | I6_15 | HG002compoundhet | homalt | 14.4522 | 100.0000 | 7.7889 | 57.4332 | 31 | 0 | 31 | 367 | 366 | 99.7275 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.6906 | 99.4825 | 97.9112 | 60.8903 | 18072 | 94 | 18047 | 385 | 366 | 95.0649 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.6906 | 99.4825 | 97.9112 | 60.8903 | 18072 | 94 | 18047 | 385 | 366 | 95.0649 | |
| raldana-dualsentieon | INDEL | I6_15 | HG002compoundhet | * | 92.3351 | 89.3573 | 95.5182 | 36.0215 | 7842 | 934 | 7843 | 368 | 366 | 99.4565 | |
| qzeng-custom | SNP | * | map_l150_m0_e0 | het | 75.9917 | 64.6851 | 92.0882 | 93.9068 | 5136 | 2804 | 5098 | 438 | 367 | 83.7900 | |
| cchapple-custom | SNP | ti | map_siren | * | 98.4477 | 98.4784 | 98.4171 | 57.2072 | 98828 | 1527 | 98796 | 1589 | 367 | 23.0963 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.1519 | 97.5866 | 98.7237 | 61.6188 | 30650 | 758 | 30631 | 396 | 367 | 92.6768 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.1519 | 97.5866 | 98.7237 | 61.6188 | 30650 | 758 | 30631 | 396 | 367 | 92.6768 | |
| gduggal-bwafb | INDEL | * | HG002complexvar | het | 96.3773 | 93.9496 | 98.9337 | 53.9146 | 43416 | 2796 | 46670 | 503 | 367 | 72.9622 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.2925 | 98.9506 | 97.6432 | 71.0801 | 17632 | 187 | 17235 | 416 | 367 | 88.2212 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 53.7099 | 42.3437 | 73.4172 | 63.2026 | 2851 | 3882 | 3850 | 1394 | 367 | 26.3271 | |
| gduggal-snapplat | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 27.4935 | 24.7277 | 30.9558 | 84.2395 | 999 | 3041 | 1276 | 2846 | 368 | 12.9304 | |
| anovak-vg | SNP | ti | map_l250_m1_e0 | * | 74.8997 | 81.6117 | 69.2079 | 91.2986 | 3737 | 842 | 3722 | 1656 | 368 | 22.2222 | |
| gduggal-bwavard | SNP | * | map_siren | het | 96.2598 | 97.0810 | 95.4524 | 69.7950 | 88335 | 2656 | 87233 | 4156 | 368 | 8.8547 | |
| gduggal-snapvard | SNP | * | map_l100_m1_e0 | het | 93.2304 | 96.7393 | 89.9672 | 77.3983 | 43880 | 1479 | 43312 | 4830 | 369 | 7.6398 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 29.6071 | 24.5130 | 37.3737 | 73.8468 | 302 | 930 | 481 | 806 | 369 | 45.7816 | |
| gduggal-snapvard | INDEL | C1_5 | * | het | 54.5455 | 100.0000 | 37.5000 | 88.8932 | 9 | 0 | 2265 | 3775 | 369 | 9.7748 | |
| gduggal-snapplat | INDEL | I1_5 | * | het | 74.5979 | 72.6661 | 76.6351 | 71.5717 | 57436 | 21605 | 58022 | 17690 | 370 | 2.0916 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.6511 | 96.9845 | 98.3269 | 41.1237 | 23800 | 740 | 23802 | 405 | 370 | 91.3580 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 64.3273 | 59.5954 | 69.8756 | 29.2072 | 1031 | 699 | 1067 | 460 | 370 | 80.4348 | |
| eyeh-varpipe | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 73.9522 | 65.2228 | 85.3794 | 65.4520 | 2635 | 1405 | 2914 | 499 | 370 | 74.1483 | |
| gduggal-snapvard | SNP | * | map_l100_m2_e0 | het | 93.3360 | 96.7693 | 90.1379 | 78.6381 | 44900 | 1499 | 44319 | 4849 | 371 | 7.6511 | |
| rpoplin-dv42 | INDEL | D6_15 | HG002compoundhet | het | 80.3742 | 96.7290 | 68.7500 | 68.2119 | 828 | 28 | 825 | 375 | 371 | 98.9333 | |
| bgallagher-sentieon | INDEL | I6_15 | * | homalt | 97.0258 | 99.8718 | 94.3376 | 54.5892 | 6231 | 8 | 6231 | 374 | 371 | 99.1979 | |
| anovak-vg | INDEL | * | map_l125_m1_e0 | * | 72.5033 | 74.1813 | 70.8995 | 87.0946 | 1563 | 544 | 1608 | 660 | 372 | 56.3636 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.2203 | 97.7012 | 98.7450 | 60.3971 | 30686 | 722 | 30686 | 390 | 372 | 95.3846 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.2203 | 97.7012 | 98.7450 | 60.3971 | 30686 | 722 | 30686 | 390 | 372 | 95.3846 | |
| gduggal-snapvard | INDEL | D16_PLUS | * | het | 17.6734 | 11.3960 | 39.3474 | 71.0797 | 360 | 2799 | 410 | 632 | 372 | 58.8608 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.2372 | 99.7214 | 96.7966 | 60.1274 | 11452 | 32 | 11452 | 379 | 372 | 98.1530 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 82.1636 | 88.4927 | 76.6793 | 63.1888 | 3599 | 468 | 3847 | 1170 | 372 | 31.7949 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 79.9918 | 88.3797 | 73.0580 | 45.8556 | 540 | 71 | 1928 | 711 | 372 | 52.3207 | |
| ndellapenna-hhga | INDEL | D16_PLUS | * | * | 85.7572 | 80.4393 | 91.8280 | 64.0820 | 5457 | 1327 | 5551 | 494 | 372 | 75.3036 | |
| ckim-isaac | INDEL | * | HG002compoundhet | homalt | 60.3591 | 67.2012 | 54.7816 | 76.0328 | 461 | 225 | 464 | 383 | 372 | 97.1279 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 78.4884 | 95.1433 | 66.7958 | 80.7253 | 1195 | 61 | 1207 | 600 | 372 | 62.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | HG002compoundhet | * | 95.8155 | 94.7855 | 96.8682 | 66.0428 | 11597 | 638 | 11599 | 375 | 373 | 99.4667 | |
| gduggal-snapvard | INDEL | C1_5 | HG002complexvar | * | 81.4638 | 100.0000 | 68.7248 | 77.2577 | 7 | 0 | 3072 | 1398 | 373 | 26.6810 | |
| gduggal-snapvard | INDEL | D16_PLUS | * | * | 10.7850 | 6.2058 | 41.1492 | 71.3717 | 421 | 6363 | 444 | 635 | 373 | 58.7402 | |
| hfeng-pmm1 | INDEL | * | * | het | 99.4245 | 99.1923 | 99.6578 | 58.3471 | 192565 | 1568 | 192194 | 660 | 374 | 56.6667 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 91.7774 | 93.1267 | 90.4666 | 45.7994 | 691 | 51 | 4033 | 425 | 374 | 88.0000 | |
| 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 | |
| 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 | |
| gduggal-bwavard | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.0548 | 97.5889 | 96.5265 | 67.4923 | 34565 | 854 | 34181 | 1230 | 375 | 30.4878 | |
| eyeh-varpipe | INDEL | I6_15 | HG002compoundhet | het | 24.7604 | 59.6154 | 15.6250 | 55.8621 | 124 | 84 | 70 | 378 | 375 | 99.2063 | |