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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
62951-63000 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.2813 | 99.1758 | 99.3872 | 70.5555 | 3730 | 31 | 3730 | 23 | 22 | 95.6522 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.2813 | 99.1758 | 99.3872 | 70.5555 | 3730 | 31 | 3730 | 23 | 22 | 95.6522 | |
| hfeng-pmm3 | SNP | * | map_l150_m1_e0 | homalt | 99.7427 | 99.7250 | 99.7604 | 71.2100 | 11242 | 31 | 11242 | 27 | 10 | 37.0370 | |
| hfeng-pmm3 | SNP | * | map_l150_m2_e0 | homalt | 99.7521 | 99.7350 | 99.7691 | 73.4090 | 11668 | 31 | 11668 | 27 | 10 | 37.0370 | |
| hfeng-pmm3 | SNP | * | map_l150_m2_e1 | homalt | 99.7548 | 99.7379 | 99.7716 | 73.4338 | 11796 | 31 | 11796 | 27 | 10 | 37.0370 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 91.5663 | 85.9729 | 97.9381 | 91.4197 | 190 | 31 | 190 | 4 | 0 | 0.0000 | |
| hfeng-pmm3 | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5487 | 99.1014 | 100.0000 | 35.3153 | 3419 | 31 | 3416 | 0 | 0 | ||
| jlack-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3167 | 99.5384 | 99.0960 | 53.8093 | 6685 | 31 | 6687 | 61 | 11 | 18.0328 | |
| hfeng-pmm1 | INDEL | I16_PLUS | HG002complexvar | * | 98.4592 | 97.6318 | 99.3007 | 66.7785 | 1278 | 31 | 1278 | 9 | 8 | 88.8889 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.1027 | 94.6827 | 99.6497 | 66.9177 | 552 | 31 | 569 | 2 | 2 | 100.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.8754 | 95.3172 | 96.4401 | 77.6815 | 631 | 31 | 596 | 22 | 12 | 54.5455 | |
| jlack-gatk | SNP | ti | HG002compoundhet | het | 99.4749 | 99.6739 | 99.2768 | 41.5881 | 9474 | 31 | 9472 | 69 | 16 | 23.1884 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6951 | 99.8992 | 99.4918 | 73.2959 | 30730 | 31 | 30737 | 157 | 151 | 96.1783 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.7687 | 94.9675 | 98.6395 | 64.7059 | 585 | 31 | 580 | 8 | 8 | 100.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.3941 | 92.5121 | 98.4615 | 73.8956 | 383 | 31 | 384 | 6 | 5 | 83.3333 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.8396 | 93.5417 | 98.2533 | 81.8470 | 449 | 31 | 450 | 8 | 7 | 87.5000 | |
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5600 | 99.2006 | 99.9221 | 57.7897 | 3847 | 31 | 3847 | 3 | 0 | 0.0000 | |
| hfeng-pmm1 | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 86.8217 | 78.3217 | 97.3913 | 92.9405 | 112 | 31 | 112 | 3 | 1 | 33.3333 | |
| hfeng-pmm2 | INDEL | * | map_l125_m2_e0 | * | 98.2547 | 98.5883 | 97.9233 | 87.9829 | 2165 | 31 | 2169 | 46 | 7 | 15.2174 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 76.1194 | 61.4458 | 100.0000 | 31.7647 | 51 | 32 | 58 | 0 | 0 | ||
| hfeng-pmm1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.3551 | 98.9186 | 99.7954 | 49.2385 | 2927 | 32 | 2927 | 6 | 0 | 0.0000 | |
| hfeng-pmm1 | SNP | tv | HG002complexvar | homalt | 99.9763 | 99.9664 | 99.9863 | 22.9407 | 95079 | 32 | 95072 | 13 | 11 | 84.6154 | |
| hfeng-pmm2 | INDEL | * | map_l125_m2_e1 | * | 98.2545 | 98.5618 | 97.9492 | 88.0799 | 2193 | 32 | 2197 | 46 | 7 | 15.2174 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.2945 | 99.6172 | 97.0064 | 59.6494 | 8328 | 32 | 8328 | 257 | 256 | 99.6109 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.2945 | 99.6172 | 97.0064 | 59.6494 | 8328 | 32 | 8328 | 257 | 256 | 99.6109 | |
| jlack-gatk | INDEL | D1_5 | map_siren | * | 96.8891 | 99.0932 | 94.7810 | 83.4660 | 3497 | 32 | 3505 | 193 | 13 | 6.7358 | |
| hfeng-pmm2 | SNP | * | map_l125_m1_e0 | homalt | 99.8078 | 99.8107 | 99.8048 | 66.6048 | 16873 | 32 | 16873 | 33 | 14 | 42.4242 | |
| hfeng-pmm2 | SNP | * | map_l125_m2_e0 | homalt | 99.8130 | 99.8158 | 99.8101 | 69.0538 | 17343 | 32 | 17343 | 33 | 14 | 42.4242 | |
| hfeng-pmm2 | SNP | * | map_l125_m2_e1 | homalt | 99.8146 | 99.8175 | 99.8118 | 69.0869 | 17500 | 32 | 17500 | 33 | 14 | 42.4242 | |
| hfeng-pmm2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 90.8723 | 85.5204 | 96.9388 | 91.1030 | 189 | 32 | 190 | 6 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | tv | HG002complexvar | homalt | 99.9732 | 99.9664 | 99.9800 | 23.0303 | 95079 | 32 | 95074 | 19 | 13 | 68.4211 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.0122 | 94.5111 | 99.6491 | 66.8219 | 551 | 32 | 568 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.0766 | 95.1952 | 99.0338 | 86.4144 | 634 | 32 | 615 | 6 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.0766 | 95.1952 | 99.0338 | 86.4144 | 634 | 32 | 615 | 6 | 0 | 0.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 99.3263 | 98.8086 | 99.8495 | 53.5477 | 2654 | 32 | 2654 | 4 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.7748 | 97.6522 | 99.9235 | 77.0526 | 1331 | 32 | 1307 | 1 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.9533 | 95.6873 | 98.2533 | 72.2760 | 710 | 32 | 675 | 12 | 7 | 58.3333 | |
| hfeng-pmm2 | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 77.3481 | 68.6275 | 88.6076 | 92.5047 | 70 | 32 | 70 | 9 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 76.9231 | 65.2174 | 93.7500 | 58.4416 | 60 | 32 | 60 | 4 | 1 | 25.0000 | |
| jlack-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.0453 | 99.0148 | 99.0758 | 65.2537 | 3216 | 32 | 3216 | 30 | 7 | 23.3333 | |
| jli-custom | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.4605 | 98.5514 | 94.4565 | 64.0006 | 2177 | 32 | 2181 | 128 | 121 | 94.5312 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.7827 | 99.6639 | 97.9169 | 51.5925 | 9489 | 32 | 9495 | 202 | 199 | 98.5149 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.4225 | 97.6048 | 97.2409 | 55.7572 | 1304 | 32 | 1304 | 37 | 14 | 37.8378 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.9376 | 96.2573 | 97.6275 | 55.5145 | 823 | 32 | 823 | 20 | 1 | 5.0000 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 76.3336 | 82.0225 | 71.3826 | 66.3055 | 146 | 32 | 222 | 89 | 24 | 26.9663 | |
| ltrigg-rtg2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.3336 | 98.6760 | 100.0000 | 74.6486 | 2385 | 32 | 2381 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0316 | 99.5706 | 98.4983 | 37.0609 | 7420 | 32 | 7412 | 113 | 2 | 1.7699 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 84.5227 | 93.4426 | 77.1574 | 75.5280 | 456 | 32 | 456 | 135 | 119 | 88.1481 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 48.0237 | 81.0651 | 34.1176 | 68.8073 | 137 | 32 | 58 | 112 | 111 | 99.1071 | |
| mlin-fermikit | INDEL | D16_PLUS | map_l100_m2_e0 | * | 59.1325 | 64.4444 | 54.6296 | 93.1904 | 58 | 32 | 59 | 49 | 15 | 30.6122 | |