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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
3251-3300 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | INDEL | I6_15 | HG002compoundhet | hetalt | 85.9482 | 75.6238 | 99.5374 | 35.2988 | 6456 | 2081 | 6455 | 30 | 20 | 66.6667 | |
| ckim-gatk | SNP | ti | map_l125_m0_e0 | homalt | 69.8436 | 53.6851 | 99.9171 | 79.2054 | 2411 | 2080 | 2411 | 2 | 1 | 50.0000 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 43.4211 | 35.2336 | 56.5657 | 54.1348 | 1131 | 2079 | 1120 | 860 | 639 | 74.3023 | |
| ckim-gatk | SNP | * | map_l250_m2_e0 | het | 73.8651 | 59.9923 | 96.0839 | 96.7509 | 3116 | 2078 | 3116 | 127 | 10 | 7.8740 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 91.6332 | 88.2406 | 95.2970 | 51.5896 | 15593 | 2078 | 16717 | 825 | 785 | 95.1515 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 91.6332 | 88.2406 | 95.2970 | 51.5896 | 15593 | 2078 | 16717 | 825 | 785 | 95.1515 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 84.4004 | 74.5748 | 97.2080 | 44.1952 | 6095 | 2078 | 6093 | 175 | 173 | 98.8571 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 42.4079 | 40.5785 | 44.4101 | 31.8353 | 1417 | 2075 | 2014 | 2521 | 2293 | 90.9560 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 35.8000 | 22.6696 | 85.0767 | 69.9119 | 608 | 2074 | 610 | 107 | 84 | 78.5047 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 93.1958 | 90.6831 | 95.8516 | 40.5987 | 20177 | 2073 | 20125 | 871 | 757 | 86.9116 | |
| ckim-isaac | INDEL | D1_5 | * | het | 97.9869 | 97.6340 | 98.3423 | 46.0249 | 85502 | 2072 | 85013 | 1433 | 986 | 68.8067 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 88.2450 | 80.8166 | 97.1772 | 89.7454 | 8729 | 2072 | 8744 | 254 | 45 | 17.7165 | |
| mlin-fermikit | SNP | * | HG002compoundhet | * | 92.7673 | 91.9758 | 93.5725 | 42.5829 | 23750 | 2072 | 23759 | 1632 | 1332 | 81.6176 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 67.9552 | 65.9379 | 70.1000 | 59.0467 | 4011 | 2072 | 3927 | 1675 | 1645 | 98.2090 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 95.3784 | 95.4685 | 95.2885 | 77.7755 | 43631 | 2071 | 43726 | 2162 | 267 | 12.3497 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 95.3784 | 95.4685 | 95.2885 | 77.7755 | 43631 | 2071 | 43726 | 2162 | 267 | 12.3497 | |
| ndellapenna-hhga | SNP | tv | * | * | 99.8629 | 99.7865 | 99.9395 | 20.8763 | 967620 | 2070 | 967646 | 586 | 175 | 29.8635 | |
| jmaeng-gatk | SNP | ti | map_l125_m0_e0 | homalt | 70.0419 | 53.9078 | 99.9587 | 78.1072 | 2421 | 2070 | 2421 | 1 | 1 | 100.0000 | |
| anovak-vg | SNP | tv | map_l125_m2_e1 | * | 80.9704 | 87.5908 | 75.2805 | 76.3445 | 14590 | 2067 | 14560 | 4781 | 1080 | 22.5894 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 0.0000 | 18.6688 | 0.0000 | 0.0000 | 474 | 2065 | 0 | 0 | 0 | ||
| ckim-isaac | INDEL | I1_5 | * | het | 97.5134 | 97.3900 | 97.6371 | 50.7018 | 76978 | 2063 | 77021 | 1864 | 1391 | 74.6245 | |
| jpowers-varprowl | SNP | tv | HG002complexvar | * | 99.3235 | 99.1623 | 99.4852 | 24.4097 | 244090 | 2062 | 244285 | 1264 | 803 | 63.5285 | |
| gduggal-snapvard | SNP | tv | HG002compoundhet | * | 76.6128 | 76.8912 | 76.3364 | 58.1709 | 6861 | 2062 | 7126 | 2209 | 1084 | 49.0720 | |
| ghariani-varprowl | SNP | tv | * | * | 98.9190 | 99.7874 | 98.0655 | 30.2667 | 967620 | 2062 | 967900 | 19093 | 1348 | 7.0602 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 82.2027 | 72.0883 | 95.6186 | 70.2749 | 5323 | 2061 | 5325 | 244 | 63 | 25.8197 | |
| ckim-gatk | SNP | tv | map_l100_m2_e1 | het | 91.5697 | 87.0686 | 96.5616 | 84.2465 | 13877 | 2061 | 13873 | 494 | 16 | 3.2389 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 82.5092 | 75.5024 | 90.9494 | 56.1947 | 6349 | 2060 | 6351 | 632 | 617 | 97.6266 | |
| ckim-gatk | SNP | tv | map_l100_m2_e0 | het | 91.4895 | 86.9494 | 96.5299 | 84.2447 | 13718 | 2059 | 13714 | 493 | 16 | 3.2454 | |
| ckim-gatk | SNP | tv | map_l100_m1_e0 | het | 91.3400 | 86.6511 | 96.5654 | 83.3110 | 13359 | 2058 | 13355 | 475 | 16 | 3.3684 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 38.7872 | 35.8879 | 42.1961 | 62.4776 | 1152 | 2058 | 1149 | 1574 | 1547 | 98.2846 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 92.7218 | 88.4618 | 97.4128 | 51.1450 | 15763 | 2056 | 30197 | 802 | 660 | 82.2943 | |
| anovak-vg | SNP | tv | map_l125_m2_e0 | * | 80.8739 | 87.5311 | 75.1578 | 76.3071 | 14433 | 2056 | 14410 | 4763 | 1075 | 22.5698 | |
| ckim-isaac | SNP | tv | map_l100_m0_e0 | homalt | 63.5928 | 46.6199 | 100.0000 | 57.1053 | 1793 | 2053 | 1793 | 0 | 0 | ||
| gduggal-snapvard | INDEL | D6_15 | HG002complexvar | * | 66.6908 | 61.3353 | 73.0708 | 52.3301 | 3252 | 2050 | 3229 | 1190 | 878 | 73.7815 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 50.1059 | 37.3855 | 75.9467 | 75.6447 | 1224 | 2050 | 1083 | 343 | 104 | 30.3207 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 40.3286 | 26.9258 | 80.2982 | 58.7796 | 755 | 2049 | 754 | 185 | 171 | 92.4324 | |
| anovak-vg | SNP | tv | map_siren | het | 83.8130 | 92.8414 | 76.3848 | 65.0646 | 26561 | 2048 | 26517 | 8198 | 1714 | 20.9075 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 40.3388 | 26.9615 | 80.0636 | 58.9286 | 756 | 2048 | 755 | 188 | 171 | 90.9574 | |
| ciseli-custom | SNP | * | map_l250_m1_e0 | het | 61.9329 | 56.9506 | 67.8706 | 93.2521 | 2708 | 2047 | 2706 | 1281 | 41 | 3.2006 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e1 | het | 91.5298 | 87.1628 | 96.3575 | 84.5264 | 13892 | 2046 | 13888 | 525 | 14 | 2.6667 | |
| mlin-fermikit | SNP | tv | map_l150_m0_e0 | het | 43.5638 | 28.0338 | 97.6716 | 69.5976 | 797 | 2046 | 797 | 19 | 0 | 0.0000 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 28.1855 | 22.9755 | 36.4514 | 63.8922 | 610 | 2045 | 982 | 1712 | 1115 | 65.1285 | |
| gduggal-bwavard | SNP | * | HG002compoundhet | het | 83.4515 | 85.5762 | 81.4296 | 49.6147 | 12133 | 2045 | 13203 | 3011 | 2546 | 84.5566 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 84.5108 | 74.7498 | 97.2039 | 41.6721 | 6051 | 2044 | 6049 | 174 | 172 | 98.8506 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 57.7611 | 43.8153 | 84.7293 | 69.3664 | 1594 | 2044 | 1487 | 268 | 182 | 67.9104 | |
| jmaeng-gatk | SNP | tv | map_l100_m2_e0 | het | 91.4492 | 87.0444 | 96.3236 | 84.5266 | 13733 | 2044 | 13729 | 524 | 14 | 2.6718 | |
| jmaeng-gatk | SNP | tv | map_l100_m1_e0 | het | 91.2990 | 86.7484 | 96.3534 | 83.6231 | 13374 | 2043 | 13370 | 506 | 14 | 2.7668 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 34.5303 | 0.0000 | 0.0000 | 1077 | 2042 | 0 | 0 | 0 | ||
| gduggal-bwaplat | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 93.5398 | 88.1295 | 99.6579 | 61.6024 | 15138 | 2039 | 15150 | 52 | 17 | 32.6923 | |
| gduggal-bwavard | INDEL | I6_15 | * | homalt | 80.3317 | 67.3345 | 99.5468 | 32.9387 | 4201 | 2038 | 4173 | 19 | 15 | 78.9474 | |