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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
801-850 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 94.2017 | 97.6736 | 90.9681 | 70.0370 | 47148 | 1123 | 48456 | 4811 | 4484 | 93.2031 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 48.9297 | 42.6581 | 57.3634 | 45.6299 | 6307 | 8478 | 6466 | 4806 | 3764 | 78.3188 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 74.7445 | 74.1265 | 75.3730 | 58.4574 | 14723 | 5139 | 14700 | 4803 | 4251 | 88.5072 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 80.9421 | 97.2812 | 69.3022 | 61.0030 | 10806 | 302 | 10816 | 4791 | 4241 | 88.5201 | |
| eyeh-varpipe | INDEL | D6_15 | * | * | 75.4633 | 71.7500 | 79.5820 | 47.2482 | 18721 | 7371 | 18658 | 4787 | 4643 | 96.9919 | |
| ciseli-custom | SNP | ti | map_l100_m2_e0 | * | 86.2627 | 83.2663 | 89.4829 | 71.0430 | 40768 | 8193 | 40704 | 4784 | 1327 | 27.7383 | |
| anovak-vg | SNP | tv | map_l125_m2_e1 | * | 80.9704 | 87.5908 | 75.2805 | 76.3445 | 14590 | 2067 | 14560 | 4781 | 1080 | 22.5894 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 58.8795 | 58.5755 | 59.1866 | 73.4509 | 4918 | 3478 | 6913 | 4767 | 1577 | 33.0816 | |
| anovak-vg | SNP | tv | map_l125_m2_e0 | * | 80.8739 | 87.5311 | 75.1578 | 76.3071 | 14433 | 2056 | 14410 | 4763 | 1075 | 22.5698 | |
| gduggal-snapvard | INDEL | D1_5 | HG002complexvar | het | 89.8124 | 96.1325 | 84.2721 | 56.4465 | 19960 | 803 | 25510 | 4761 | 3355 | 70.4684 | |
| ghariani-varprowl | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 95.4136 | 99.0024 | 92.0759 | 67.6063 | 55076 | 555 | 55287 | 4758 | 565 | 11.8747 | |
| anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 76.0027 | 83.0403 | 70.0649 | 36.4124 | 8642 | 1765 | 11127 | 4754 | 3440 | 72.3601 | |
| gduggal-snapfb | SNP | * | * | homalt | 99.6988 | 99.7992 | 99.5986 | 21.4529 | 1177792 | 2370 | 1177860 | 4747 | 451 | 9.5007 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 38.9448 | 36.3079 | 41.9946 | 48.7568 | 3434 | 6024 | 3436 | 4746 | 4690 | 98.8201 | |
| jpowers-varprowl | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 71.4050 | 68.7947 | 74.2213 | 55.0266 | 13664 | 6198 | 13653 | 4742 | 4639 | 97.8279 | |
| anovak-vg | SNP | tv | map_l125_m2_e1 | het | 77.4408 | 91.5759 | 67.0858 | 78.0971 | 9664 | 889 | 9657 | 4738 | 1048 | 22.1190 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 36.9719 | 33.9924 | 40.5239 | 46.0310 | 3215 | 6243 | 3218 | 4723 | 4680 | 99.0896 | |
| anovak-vg | SNP | tv | map_l125_m2_e0 | het | 77.3239 | 91.5342 | 66.9329 | 78.0559 | 9558 | 884 | 9554 | 4720 | 1043 | 22.0975 | |
| ciseli-custom | SNP | ti | map_l100_m1_e0 | * | 86.1026 | 83.0465 | 89.3922 | 69.2811 | 39805 | 8126 | 39742 | 4716 | 1317 | 27.9262 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 85.0606 | 95.7652 | 76.5084 | 52.6827 | 13998 | 619 | 15343 | 4711 | 4543 | 96.4339 | |
| anovak-vg | SNP | tv | map_l125_m1_e0 | * | 80.6396 | 87.4563 | 74.8088 | 74.7170 | 14007 | 2009 | 13984 | 4709 | 1051 | 22.3190 | |
| anovak-vg | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 45.9396 | 39.7316 | 54.4469 | 43.4180 | 5477 | 8308 | 5626 | 4707 | 3701 | 78.6276 | |
| ciseli-custom | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 86.4138 | 96.3627 | 78.3270 | 66.2442 | 16929 | 639 | 17004 | 4705 | 98 | 2.0829 | |
| qzeng-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 91.8743 | 94.4038 | 89.4769 | 44.0923 | 13799 | 818 | 39955 | 4699 | 3029 | 64.4605 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 34.7483 | 93.6728 | 21.3304 | 80.5514 | 1214 | 82 | 1273 | 4695 | 107 | 2.2790 | |
| gduggal-snapfb | SNP | ti | HG002complexvar | het | 99.0494 | 99.5771 | 98.5273 | 20.1517 | 313435 | 1331 | 313897 | 4692 | 557 | 11.8713 | |
| ciseli-custom | SNP | * | map_l150_m2_e1 | * | 78.3942 | 73.8684 | 83.5109 | 81.5923 | 23793 | 8417 | 23753 | 4690 | 1163 | 24.7974 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 47.2088 | 43.9090 | 51.0447 | 54.2294 | 4866 | 6216 | 4886 | 4686 | 4047 | 86.3636 | |
| qzeng-custom | INDEL | * | HG002compoundhet | het | 90.0667 | 93.8691 | 86.5604 | 55.7571 | 3843 | 251 | 30091 | 4672 | 2782 | 59.5462 | |
| ciseli-custom | INDEL | I1_5 | HG002compoundhet | homalt | 9.7782 | 77.5076 | 5.2183 | 58.7244 | 255 | 74 | 257 | 4668 | 4563 | 97.7506 | |
| anovak-vg | SNP | tv | map_l125_m1_e0 | het | 77.0260 | 91.5169 | 66.4968 | 76.6933 | 9267 | 859 | 9265 | 4668 | 1021 | 21.8723 | |
| ciseli-custom | SNP | * | map_l150_m2_e0 | * | 78.3493 | 73.8101 | 83.4833 | 81.5713 | 23510 | 8342 | 23473 | 4644 | 1150 | 24.7631 | |
| ciseli-custom | SNP | ti | map_siren | het | 88.8574 | 85.8902 | 92.0370 | 60.6835 | 53580 | 8802 | 53468 | 4626 | 118 | 2.5508 | |
| ciseli-custom | INDEL | D6_15 | HG002compoundhet | homalt | 0.9875 | 87.5000 | 0.4965 | 31.5704 | 21 | 3 | 23 | 4609 | 4348 | 94.3372 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 74.5124 | 79.7221 | 69.9419 | 60.7095 | 9982 | 2539 | 10713 | 4604 | 2731 | 59.3180 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 81.5434 | 97.2452 | 70.2073 | 58.5180 | 10802 | 306 | 10840 | 4600 | 4440 | 96.5217 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 71.3041 | 72.8754 | 69.7991 | 45.2762 | 8095 | 3013 | 10629 | 4599 | 3296 | 71.6678 | |
| jpowers-varprowl | INDEL | * | HG002complexvar | het | 92.4718 | 94.5577 | 90.4760 | 57.5873 | 43697 | 2515 | 43680 | 4598 | 4462 | 97.0422 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 57.2013 | 57.5771 | 56.8303 | 44.8249 | 3978 | 2931 | 6053 | 4598 | 4136 | 89.9522 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 66.7149 | 82.5790 | 55.9638 | 44.4510 | 1332 | 281 | 5818 | 4578 | 4118 | 89.9519 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 33.2123 | 28.3742 | 40.0394 | 54.5997 | 1726 | 4357 | 3049 | 4566 | 3071 | 67.2580 | |
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 92.5410 | 98.7028 | 87.1034 | 79.6250 | 30739 | 404 | 30832 | 4565 | 319 | 6.9880 | |
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 92.5410 | 98.7028 | 87.1034 | 79.6250 | 30739 | 404 | 30832 | 4565 | 319 | 6.9880 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 44.8798 | 37.6755 | 55.4905 | 73.6943 | 4185 | 6923 | 5685 | 4560 | 444 | 9.7368 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 44.6735 | 50.6428 | 39.9631 | 53.8471 | 1103 | 1075 | 3030 | 4552 | 3067 | 67.3770 | |
| gduggal-snapvard | SNP | ti | HG002complexvar | * | 97.8937 | 96.7473 | 99.0676 | 19.7850 | 491898 | 16538 | 483039 | 4546 | 1783 | 39.2213 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 40.2625 | 37.4075 | 43.5894 | 47.0109 | 3538 | 5920 | 3512 | 4545 | 4494 | 98.8779 | |
| ciseli-custom | SNP | tv | HG002compoundhet | het | 56.8474 | 77.9585 | 44.7336 | 53.7648 | 3643 | 1030 | 3678 | 4544 | 89 | 1.9586 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 53.6228 | 97.3655 | 37.0000 | 47.7504 | 2661 | 72 | 2664 | 4536 | 4487 | 98.9198 | |
| ciseli-custom | SNP | * | map_l150_m1_e0 | * | 77.9234 | 73.3052 | 83.1626 | 80.2472 | 22438 | 8171 | 22404 | 4536 | 1124 | 24.7795 | |