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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1051-1100 / 86044 show all | |||||||||||||||
| ciseli-custom | SNP | * | map_siren | homalt | 93.3935 | 93.4404 | 93.3467 | 52.8475 | 51538 | 3618 | 51210 | 3650 | 2749 | 75.3151 | |
| gduggal-snapvard | SNP | * | map_l100_m0_e0 | het | 90.2047 | 96.4159 | 84.7453 | 80.5659 | 20445 | 760 | 20216 | 3639 | 248 | 6.8151 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 23.7492 | 32.3709 | 18.7542 | 83.9944 | 796 | 1663 | 840 | 3639 | 38 | 1.0442 | |
| ciseli-custom | SNP | ti | map_l125_m1_e0 | * | 81.8023 | 77.7842 | 86.2580 | 75.7269 | 22818 | 6517 | 22798 | 3632 | 966 | 26.5969 | |
| egarrison-hhga | INDEL | D1_5 | HG002compoundhet | * | 69.0217 | 68.1406 | 69.9260 | 60.9500 | 8337 | 3898 | 8410 | 3617 | 3521 | 97.3459 | |
| qzeng-custom | SNP | ti | * | het | 99.4567 | 99.1981 | 99.7166 | 23.5601 | 1271618 | 10279 | 1269681 | 3608 | 520 | 14.4124 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 88.6622 | 97.0558 | 81.6049 | 51.6846 | 15296 | 464 | 15997 | 3606 | 3454 | 95.7848 | |
| gduggal-bwaplat | SNP | * | HG002compoundhet | * | 88.4972 | 90.4035 | 86.6696 | 48.3543 | 23344 | 2478 | 23445 | 3606 | 414 | 11.4809 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 79.9546 | 88.8056 | 72.7080 | 46.5949 | 9242 | 1165 | 9596 | 3602 | 1710 | 47.4736 | |
| ciseli-custom | INDEL | I6_15 | * | * | 35.4599 | 24.6948 | 62.8636 | 46.3768 | 6130 | 18693 | 6094 | 3600 | 3400 | 94.4444 | |
| ckim-isaac | INDEL | * | HG002compoundhet | * | 82.5676 | 79.0154 | 86.4543 | 46.0363 | 23673 | 6287 | 22964 | 3598 | 3236 | 89.9389 | |
| ciseli-custom | SNP | * | HG002compoundhet | homalt | 82.3846 | 93.4613 | 73.6552 | 42.1506 | 10077 | 705 | 10037 | 3590 | 971 | 27.0474 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 62.8790 | 57.8527 | 68.8617 | 41.8554 | 7975 | 5810 | 7937 | 3589 | 3504 | 97.6317 | |
| mlin-fermikit | SNP | ti | map_siren | homalt | 85.5625 | 81.8362 | 89.6443 | 44.4398 | 31029 | 6887 | 31025 | 3584 | 3486 | 97.2656 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 89.0060 | 88.0657 | 89.9667 | 48.3054 | 32225 | 4367 | 32137 | 3584 | 3498 | 97.6004 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 34.5163 | 33.2073 | 35.9327 | 70.3914 | 2020 | 4063 | 2009 | 3582 | 3513 | 98.0737 | |
| ciseli-custom | SNP | tv | map_siren | het | 84.4100 | 82.1595 | 86.7874 | 65.3031 | 23505 | 5104 | 23489 | 3576 | 93 | 2.6007 | |
| jpowers-varprowl | SNP | * | * | homalt | 99.8292 | 99.9606 | 99.6981 | 20.3193 | 1179696 | 465 | 1179822 | 3573 | 2211 | 61.8808 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 74.4014 | 87.0872 | 64.9416 | 71.9724 | 5591 | 829 | 6613 | 3570 | 542 | 15.1821 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 74.4014 | 87.0872 | 64.9416 | 71.9724 | 5591 | 829 | 6613 | 3570 | 542 | 15.1821 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 87.7692 | 97.8411 | 79.5775 | 59.2240 | 13460 | 297 | 13899 | 3567 | 3388 | 94.9818 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 87.7692 | 97.8411 | 79.5775 | 59.2240 | 13460 | 297 | 13899 | 3567 | 3388 | 94.9818 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 93.9899 | 93.5543 | 94.4295 | 71.2140 | 60278 | 4153 | 60365 | 3561 | 3233 | 90.7891 | |
| anovak-vg | INDEL | D6_15 | HG002compoundhet | * | 33.7576 | 27.6935 | 43.2221 | 33.8439 | 2501 | 6530 | 2707 | 3556 | 2531 | 71.1755 | |
| eyeh-varpipe | INDEL | D6_15 | HG002compoundhet | homalt | 1.5501 | 83.3333 | 0.7823 | 29.2688 | 20 | 4 | 28 | 3551 | 3544 | 99.8029 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 82.8096 | 94.2598 | 73.8399 | 86.2952 | 10181 | 620 | 10009 | 3546 | 141 | 3.9763 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 56.5143 | 51.2341 | 63.0078 | 48.1760 | 4878 | 4643 | 6033 | 3542 | 2746 | 77.5268 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 33.5783 | 32.0401 | 35.2715 | 61.6614 | 1949 | 4134 | 1929 | 3540 | 3386 | 95.6497 | |
| gduggal-snapvard | SNP | ti | HG002compoundhet | * | 79.9822 | 79.9565 | 80.0079 | 49.1293 | 13974 | 3503 | 14163 | 3539 | 1489 | 42.0740 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 47.4256 | 81.8182 | 33.3900 | 61.2010 | 1782 | 396 | 1769 | 3529 | 3376 | 95.6645 | |
| anovak-vg | SNP | tv | map_l150_m2_e1 | * | 79.4082 | 86.0633 | 73.7085 | 80.2069 | 9899 | 1603 | 9888 | 3527 | 846 | 23.9864 | |
| anovak-vg | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 46.7905 | 46.8317 | 46.7493 | 53.6445 | 1892 | 2148 | 3092 | 3522 | 2706 | 76.8313 | |
| anovak-vg | SNP | tv | map_l150_m2_e0 | * | 79.2839 | 86.0062 | 73.5363 | 80.1925 | 9766 | 1589 | 9759 | 3512 | 838 | 23.8610 | |
| gduggal-snapvard | SNP | ti | map_siren | * | 96.3076 | 96.1556 | 96.4600 | 63.8276 | 96497 | 3858 | 95534 | 3506 | 409 | 11.6657 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 49.1300 | 84.7567 | 34.5903 | 59.0099 | 1846 | 332 | 1853 | 3504 | 3453 | 98.5445 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 65.9412 | 85.6091 | 53.6220 | 35.4284 | 4069 | 684 | 4049 | 3502 | 3279 | 93.6322 | |
| anovak-vg | SNP | tv | map_l150_m2_e1 | het | 76.1119 | 90.7050 | 65.5638 | 81.6339 | 6665 | 683 | 6658 | 3497 | 823 | 23.5345 | |
| gduggal-snapfb | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 90.7849 | 98.9826 | 83.8412 | 55.2905 | 17998 | 185 | 18103 | 3489 | 157 | 4.4999 | |
| anovak-vg | SNP | tv | map_l150_m2_e0 | het | 75.9484 | 90.6371 | 65.3567 | 81.6125 | 6573 | 679 | 6569 | 3482 | 815 | 23.4061 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 88.8266 | 96.5799 | 82.2256 | 51.6201 | 15221 | 539 | 16108 | 3482 | 3306 | 94.9454 | |
| eyeh-varpipe | INDEL | I1_5 | HG002compoundhet | * | 54.5656 | 48.0495 | 63.1261 | 63.8199 | 5937 | 6419 | 5961 | 3482 | 3440 | 98.7938 | |
| 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-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 76.8075 | 94.3048 | 64.7869 | 87.6558 | 6491 | 392 | 6399 | 3478 | 109 | 3.1340 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 70.9466 | 66.7041 | 75.7654 | 53.5142 | 10704 | 5343 | 10864 | 3475 | 3422 | 98.4748 | |
| anovak-vg | INDEL | I6_15 | * | het | 35.7228 | 26.3530 | 55.4313 | 44.2246 | 2644 | 7389 | 4312 | 3467 | 1789 | 51.6008 | |
| ndellapenna-hhga | INDEL | D1_5 | HG002compoundhet | * | 69.2944 | 67.8709 | 70.7788 | 60.8775 | 8304 | 3931 | 8388 | 3463 | 3380 | 97.6032 | |
| gduggal-bwavard | SNP | * | HG002complexvar | * | 98.3118 | 97.1354 | 99.5171 | 19.6107 | 732775 | 21610 | 712182 | 3456 | 2272 | 65.7407 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 29.0460 | 26.6974 | 31.8478 | 58.4515 | 1624 | 4459 | 1615 | 3456 | 3422 | 99.0162 | |
| gduggal-snapvard | SNP | ti | HG002compoundhet | het | 77.4625 | 83.1755 | 72.4839 | 53.3720 | 7905 | 1599 | 9096 | 3453 | 1426 | 41.2974 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 83.6346 | 82.9843 | 84.2953 | 47.3907 | 18464 | 3786 | 18534 | 3453 | 3234 | 93.6577 | |