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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
70801-70850 / 86044 show all | |||||||||||||||
| ckim-dragen | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8088 | 99.7806 | 99.8371 | 58.7309 | 28198 | 62 | 28192 | 46 | 19 | 41.3043 | |
| ckim-dragen | INDEL | * | map_l150_m1_e0 | het | 95.1716 | 95.6725 | 94.6759 | 91.3591 | 818 | 37 | 818 | 46 | 5 | 10.8696 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.3619 | 97.5940 | 91.3371 | 87.9208 | 649 | 16 | 485 | 46 | 31 | 67.3913 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.5673 | 97.5168 | 97.6178 | 66.9009 | 1885 | 48 | 1885 | 46 | 46 | 100.0000 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.3536 | 99.3753 | 99.3320 | 81.7241 | 6840 | 43 | 6840 | 46 | 15 | 32.6087 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.2854 | 93.2411 | 99.5352 | 28.3262 | 9767 | 708 | 9850 | 46 | 46 | 100.0000 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.1191 | 96.5339 | 97.7114 | 58.6675 | 1866 | 67 | 1964 | 46 | 42 | 91.3043 | |
| cchapple-custom | INDEL | I16_PLUS | * | het | 98.4654 | 97.8293 | 99.1099 | 69.2948 | 2659 | 59 | 5122 | 46 | 28 | 60.8696 | |
| ckim-dragen | INDEL | D1_5 | * | hetalt | 96.7193 | 94.0654 | 99.5273 | 61.7567 | 9637 | 608 | 9685 | 46 | 46 | 100.0000 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.4368 | 99.3178 | 99.5561 | 50.0867 | 10336 | 71 | 10317 | 46 | 37 | 80.4348 | |
| ckim-dragen | INDEL | I1_5 | map_siren | het | 97.4161 | 97.5610 | 97.2716 | 82.6203 | 1640 | 41 | 1640 | 46 | 8 | 17.3913 | |
| ckim-dragen | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.3007 | 99.0279 | 99.5750 | 78.5377 | 10696 | 105 | 10777 | 46 | 21 | 45.6522 | |
| eyeh-varpipe | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 50.6572 | 90.2439 | 35.2113 | 79.8867 | 37 | 4 | 25 | 46 | 14 | 30.4348 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 90.5642 | 94.2559 | 87.1508 | 72.0313 | 361 | 22 | 312 | 46 | 20 | 43.4783 | |
| gduggal-bwavard | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 0.0000 | 0.0000 | 57.0093 | 94.1144 | 0 | 0 | 61 | 46 | 4 | 8.6957 | |
| gduggal-bwavard | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 0.0000 | 0.0000 | 55.3398 | 93.8763 | 0 | 0 | 57 | 46 | 4 | 8.6957 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 64.9523 | 50.2994 | 91.6515 | 76.9456 | 504 | 498 | 505 | 46 | 8 | 17.3913 | |
| gduggal-bwaplat | INDEL | I6_15 | HG002complexvar | het | 84.5433 | 74.6497 | 97.4600 | 66.9103 | 1758 | 597 | 1765 | 46 | 16 | 34.7826 | |
| gduggal-bwaplat | SNP | * | func_cds | * | 99.4779 | 99.2121 | 99.7452 | 34.2475 | 18007 | 143 | 18007 | 46 | 4 | 8.6957 | |
| gduggal-bwaplat | SNP | * | func_cds | het | 99.4076 | 99.2295 | 99.5864 | 39.9773 | 11075 | 86 | 11075 | 46 | 4 | 8.6957 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 83.9148 | 73.4651 | 97.8302 | 47.7704 | 706 | 255 | 2074 | 46 | 36 | 78.2609 | |
| hfeng-pmm1 | SNP | ti | map_l150_m0_e0 | het | 98.8393 | 98.5874 | 99.0925 | 80.9472 | 5025 | 72 | 5023 | 46 | 8 | 17.3913 | |
| hfeng-pmm1 | SNP | tv | map_l100_m1_e0 | het | 99.4603 | 99.2216 | 99.7001 | 64.9458 | 15297 | 120 | 15293 | 46 | 12 | 26.0870 | |
| hfeng-pmm1 | SNP | tv | map_l125_m0_e0 | * | 99.1084 | 98.9142 | 99.3035 | 75.2093 | 6559 | 72 | 6558 | 46 | 13 | 28.2609 | |
| hfeng-pmm2 | INDEL | * | map_l125_m2_e0 | * | 98.2547 | 98.5883 | 97.9233 | 87.9829 | 2165 | 31 | 2169 | 46 | 7 | 15.2174 | |
| hfeng-pmm2 | INDEL | * | map_l125_m2_e1 | * | 98.2545 | 98.5618 | 97.9492 | 88.0799 | 2193 | 32 | 2197 | 46 | 7 | 15.2174 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.5934 | 95.8965 | 99.3515 | 52.0127 | 7081 | 303 | 7047 | 46 | 40 | 86.9565 | |
| hfeng-pmm3 | INDEL | D6_15 | HG002compoundhet | homalt | 51.0638 | 100.0000 | 34.2857 | 66.3462 | 24 | 0 | 24 | 46 | 45 | 97.8261 | |
| hfeng-pmm3 | INDEL | I16_PLUS | HG002compoundhet | * | 95.0875 | 92.5805 | 97.7340 | 52.1790 | 1984 | 159 | 1984 | 46 | 45 | 97.8261 | |
| hfeng-pmm3 | SNP | tv | map_l100_m0_e0 | het | 99.3072 | 99.2523 | 99.3623 | 70.7621 | 7168 | 54 | 7167 | 46 | 4 | 8.6957 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 95.8359 | 92.4591 | 99.4688 | 63.5748 | 8595 | 701 | 8613 | 46 | 42 | 91.3043 | |
| jlack-gatk | INDEL | I1_5 | map_l125_m1_e0 | * | 96.5825 | 98.5542 | 94.6882 | 89.3152 | 818 | 12 | 820 | 46 | 4 | 8.6957 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.5254 | 99.5254 | 99.5254 | 68.0722 | 9646 | 46 | 9646 | 46 | 24 | 52.1739 | |
| hfeng-pmm3 | INDEL | D1_5 | HG002compoundhet | het | 87.8989 | 80.4977 | 96.7989 | 73.8775 | 1391 | 337 | 1391 | 46 | 42 | 91.3043 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.8735 | 96.4965 | 99.2905 | 49.4936 | 6445 | 234 | 6437 | 46 | 35 | 76.0870 | |
| hfeng-pmm1 | INDEL | I1_5 | HG002complexvar | * | 99.5778 | 99.2956 | 99.8615 | 56.6148 | 33128 | 235 | 33171 | 46 | 29 | 63.0435 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 91.5617 | 96.6667 | 86.9688 | 73.4387 | 319 | 11 | 307 | 46 | 35 | 76.0870 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 93.7500 | 98.9446 | 89.0736 | 60.1703 | 375 | 4 | 375 | 46 | 46 | 100.0000 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.4252 | 92.3274 | 98.7380 | 54.1740 | 3598 | 299 | 3599 | 46 | 39 | 84.7826 | |
| rpoplin-dv42 | SNP | tv | map_l250_m1_e0 | * | 97.8376 | 97.4311 | 98.2476 | 86.7964 | 2579 | 68 | 2579 | 46 | 30 | 65.2174 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 0.0000 | 0.0000 | 65.9259 | 0 | 0 | 0 | 46 | 1 | 2.1739 | ||
| gduggal-snapvard | INDEL | D6_15 | map_l125_m1_e0 | het | 77.8579 | 87.5000 | 70.1299 | 85.8326 | 56 | 8 | 108 | 46 | 30 | 65.2174 | |
| gduggal-snapvard | INDEL | I1_5 | map_l250_m2_e0 | het | 80.7151 | 96.9697 | 69.1275 | 96.5865 | 64 | 2 | 103 | 46 | 12 | 26.0870 | |
| gduggal-snapvard | INDEL | I1_5 | map_l250_m2_e1 | het | 80.7151 | 96.9697 | 69.1275 | 96.6682 | 64 | 2 | 103 | 46 | 12 | 26.0870 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 68.4689 | 57.9334 | 83.6879 | 54.1463 | 1026 | 745 | 236 | 46 | 44 | 95.6522 | |
| gduggal-snapfb | SNP | * | map_l125_m0_e0 | homalt | 96.2940 | 93.4893 | 99.2723 | 82.1168 | 6275 | 437 | 6275 | 46 | 16 | 34.7826 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 95.3327 | 99.7921 | 91.2548 | 72.8866 | 480 | 1 | 480 | 46 | 1 | 2.1739 | |
| gduggal-snapfb | SNP | tv | map_l100_m1_e0 | homalt | 98.3618 | 97.2686 | 99.4798 | 71.8035 | 8796 | 247 | 8797 | 46 | 9 | 19.5652 | |
| gduggal-snapfb | SNP | tv | map_l100_m2_e0 | homalt | 98.3869 | 97.3084 | 99.4896 | 73.1420 | 8966 | 248 | 8967 | 46 | 9 | 19.5652 | |
| gduggal-snapfb | SNP | tv | map_l100_m2_e1 | homalt | 98.4024 | 97.3339 | 99.4946 | 73.1383 | 9054 | 248 | 9055 | 46 | 9 | 19.5652 | |