PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
751-800 / 86044 show all | |||||||||||||||
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 0.0000 | 0.5382 | 0.0000 | 0.0000 | 50 | 9241 | 0 | 0 | 0 | ||
| ghariani-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 0.0000 | 0.5382 | 0.0000 | 0.0000 | 50 | 9241 | 0 | 0 | 0 | ||
| ghariani-varprowl | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 0.6024 | 0.0000 | 0.0000 | 56 | 9240 | 0 | 0 | 0 | ||
| gduggal-bwaplat | SNP | ti | map_l100_m0_e0 | * | 72.8908 | 57.5582 | 99.3581 | 86.0136 | 12531 | 9240 | 12537 | 81 | 26 | 32.0988 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 40.8104 | 37.5245 | 44.7270 | 52.3629 | 5548 | 9237 | 5505 | 6803 | 6744 | 99.1327 | |
| gduggal-snapfb | INDEL | * | HG002complexvar | * | 90.4920 | 87.9994 | 93.1300 | 55.3026 | 67705 | 9233 | 69298 | 5112 | 2371 | 46.3811 | |
| ckim-gatk | SNP | * | map_l100_m0_e0 | * | 82.8691 | 71.9040 | 97.7802 | 83.9171 | 23614 | 9227 | 23610 | 536 | 48 | 8.9552 | |
| eyeh-varpipe | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 56.5705 | 40.1699 | 95.6035 | 76.3129 | 6193 | 9224 | 10155 | 467 | 451 | 96.5739 | |
| jmaeng-gatk | SNP | * | map_l100_m0_e0 | * | 82.8475 | 71.9345 | 97.6638 | 84.1509 | 23624 | 9217 | 23620 | 565 | 48 | 8.4956 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 70.3371 | 62.5265 | 80.3777 | 56.0717 | 15344 | 9196 | 18388 | 4489 | 2592 | 57.7411 | |
| gduggal-bwaplat | SNP | ti | HG002complexvar | het | 97.7064 | 97.0801 | 98.3410 | 19.6959 | 305575 | 9191 | 306161 | 5165 | 589 | 11.4037 | |
| qzeng-custom | SNP | * | map_l100_m0_e0 | * | 82.6366 | 72.0228 | 96.9194 | 83.3401 | 23653 | 9188 | 23407 | 744 | 630 | 84.6774 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 89.8755 | 85.9451 | 94.1826 | 54.7512 | 56166 | 9185 | 55450 | 3425 | 2525 | 73.7226 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 89.8755 | 85.9451 | 94.1826 | 54.7512 | 56166 | 9185 | 55450 | 3425 | 2525 | 73.7226 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 87.1515 | 85.9467 | 88.3906 | 61.9558 | 56167 | 9184 | 55976 | 7352 | 7082 | 96.3275 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 87.1515 | 85.9467 | 88.3906 | 61.9558 | 56167 | 9184 | 55976 | 7352 | 7082 | 96.3275 | |
| eyeh-varpipe | INDEL | I6_15 | * | * | 71.2994 | 63.0343 | 82.0590 | 39.8519 | 15647 | 9176 | 15734 | 3440 | 3408 | 99.0698 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 73.1589 | 71.4116 | 74.9939 | 43.9770 | 22846 | 9146 | 33793 | 11268 | 11182 | 99.2368 | |
| ckim-vqsr | SNP | * | map_l125_m2_e1 | het | 81.3082 | 69.1532 | 98.6474 | 89.1453 | 20497 | 9143 | 20494 | 281 | 4 | 1.4235 | |
| mlin-fermikit | INDEL | * | * | hetalt | 77.7361 | 63.8348 | 99.3774 | 60.1130 | 16110 | 9127 | 16282 | 102 | 100 | 98.0392 | |
| mlin-fermikit | INDEL | * | HG002compoundhet | hetalt | 77.7377 | 63.7887 | 99.4948 | 53.3255 | 16062 | 9118 | 16150 | 82 | 81 | 98.7805 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 37.1023 | 33.8847 | 40.9951 | 49.8226 | 4671 | 9114 | 4639 | 6677 | 6648 | 99.5657 | |
| gduggal-bwaplat | INDEL | * | HG002compoundhet | * | 80.3779 | 69.5961 | 95.1127 | 70.6361 | 20851 | 9109 | 20843 | 1071 | 677 | 63.2120 | |
| ckim-vqsr | SNP | * | map_l125_m2_e0 | het | 81.2064 | 69.0122 | 98.6348 | 89.1411 | 20233 | 9085 | 20230 | 280 | 4 | 1.4286 | |
| asubramanian-gatk | SNP | * | map_l150_m1_e0 | homalt | 32.6455 | 19.5068 | 100.0000 | 91.9371 | 2199 | 9074 | 2199 | 0 | 0 | ||
| ghariani-varprowl | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 46.6247 | 43.6219 | 50.0715 | 62.1939 | 7000 | 9047 | 7003 | 6983 | 6898 | 98.7828 | |
| ckim-gatk | SNP | * | map_siren | homalt | 91.0516 | 83.5974 | 99.9653 | 55.1658 | 46109 | 9047 | 46100 | 16 | 14 | 87.5000 | |
| asubramanian-gatk | SNP | ti | map_l150_m1_e0 | het | 42.4790 | 26.9846 | 99.7608 | 94.8360 | 3338 | 9032 | 3336 | 8 | 4 | 50.0000 | |
| gduggal-bwaplat | INDEL | D1_5 | * | het | 94.1987 | 89.7070 | 99.1640 | 66.4739 | 78560 | 9014 | 78527 | 662 | 219 | 33.0816 | |
| ckim-isaac | SNP | ti | map_l150_m2_e1 | * | 72.1848 | 56.5603 | 99.7362 | 77.6680 | 11721 | 9002 | 11721 | 31 | 7 | 22.5806 | |
| gduggal-snapfb | INDEL | * | * | hetalt | 71.6867 | 64.3698 | 80.8803 | 78.7792 | 16245 | 8992 | 5770 | 1364 | 830 | 60.8504 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 51.1782 | 35.9607 | 88.7235 | 60.7545 | 5046 | 8986 | 5067 | 644 | 550 | 85.4037 | |
| jmaeng-gatk | SNP | * | map_siren | homalt | 91.1261 | 83.7262 | 99.9610 | 54.5250 | 46180 | 8976 | 46171 | 18 | 18 | 100.0000 | |
| gduggal-snapfb | INDEL | * | HG002compoundhet | hetalt | 76.0060 | 64.4003 | 92.7141 | 74.7872 | 16216 | 8964 | 5739 | 451 | 378 | 83.8137 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 64.5118 | 50.6716 | 88.7536 | 66.8832 | 9205 | 8961 | 9186 | 1164 | 976 | 83.8488 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 64.5118 | 50.6716 | 88.7536 | 66.8832 | 9205 | 8961 | 9186 | 1164 | 976 | 83.8488 | |
| ckim-vqsr | SNP | * | map_l125_m1_e0 | het | 80.8165 | 68.4629 | 98.6098 | 88.4760 | 19438 | 8954 | 19435 | 274 | 3 | 1.0949 | |
| mlin-fermikit | SNP | tv | map_siren | het | 80.8694 | 68.7161 | 98.2452 | 51.7745 | 19659 | 8950 | 19651 | 351 | 3 | 0.8547 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 64.6659 | 50.7487 | 89.1009 | 66.3976 | 9219 | 8947 | 9197 | 1125 | 989 | 87.9111 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 64.6659 | 50.7487 | 89.1009 | 66.3976 | 9219 | 8947 | 9197 | 1125 | 989 | 87.9111 | |
| ckim-isaac | INDEL | * | HG002complexvar | * | 91.9300 | 88.4153 | 95.7357 | 48.5598 | 68025 | 8913 | 67037 | 2986 | 1352 | 45.2780 | |
| ckim-isaac | SNP | ti | map_l150_m2_e0 | * | 72.1859 | 56.5571 | 99.7506 | 77.5984 | 11601 | 8911 | 11601 | 29 | 5 | 17.2414 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 55.1228 | 49.5784 | 62.0635 | 51.0444 | 8761 | 8910 | 8975 | 5486 | 4728 | 86.1830 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 55.1228 | 49.5784 | 62.0635 | 51.0444 | 8761 | 8910 | 8975 | 5486 | 4728 | 86.1830 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 0.0000 | 46.7074 | 0.0000 | 0.0000 | 7802 | 8902 | 0 | 0 | 0 | ||
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 0.0000 | 46.7074 | 0.0000 | 0.0000 | 7802 | 8902 | 0 | 0 | 0 | ||
| ckim-isaac | SNP | ti | map_l100_m2_e1 | het | 83.1462 | 71.2597 | 99.7920 | 67.1300 | 22062 | 8898 | 22066 | 46 | 4 | 8.6957 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 47.5340 | 42.9094 | 53.2758 | 84.2729 | 6684 | 8893 | 6855 | 6012 | 485 | 8.0672 | |
| gduggal-bwaplat | INDEL | I1_5 | * | het | 93.5751 | 88.7894 | 98.9060 | 66.7915 | 70180 | 8861 | 70159 | 776 | 424 | 54.6392 | |
| mlin-fermikit | SNP | * | map_l100_m2_e1 | homalt | 74.4467 | 68.1285 | 82.0565 | 52.6294 | 18937 | 8859 | 18937 | 4141 | 3961 | 95.6532 | |