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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
8851-8900 / 86044 show all | |||||||||||||||
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 31.5161 | 18.7373 | 99.1071 | 42.5641 | 92 | 399 | 111 | 1 | 1 | 100.0000 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 0.0000 | 9.1116 | 0.0000 | 0.0000 | 40 | 399 | 0 | 0 | 0 | ||
| astatham-gatk | SNP | * | segdup | * | 99.1969 | 98.5784 | 99.8232 | 90.3648 | 27668 | 399 | 27662 | 49 | 12 | 24.4898 | |
| asubramanian-gatk | INDEL | I16_PLUS | * | * | 95.8942 | 93.7431 | 98.1463 | 72.1669 | 5978 | 399 | 5983 | 113 | 95 | 84.0708 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.2264 | 95.2551 | 99.2811 | 61.5901 | 8010 | 399 | 8010 | 58 | 49 | 84.4828 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 0.0000 | 95.7078 | 0.0000 | 0.0000 | 8897 | 399 | 0 | 0 | 0 | ||
| eyeh-varpipe | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 78.4487 | 74.1077 | 83.3299 | 46.2271 | 1142 | 399 | 4044 | 809 | 800 | 98.8875 | |
| jlack-gatk | INDEL | I1_5 | * | het | 99.1970 | 99.4952 | 98.9006 | 61.6913 | 78642 | 399 | 78625 | 874 | 231 | 26.4302 | |
| hfeng-pmm2 | INDEL | I1_5 | * | het | 99.6023 | 99.4952 | 99.7096 | 59.9116 | 78642 | 399 | 78624 | 229 | 130 | 56.7686 | |
| gduggal-snapfb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 399 | 0 | 0 | 0 | |||
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 60.8435 | 85.3147 | 47.2815 | 88.9072 | 2318 | 399 | 2261 | 2521 | 114 | 4.5220 | |
| gduggal-snapplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 399 | 0 | 0 | 0 | |||
| gduggal-snapplat | INDEL | D1_5 | map_siren | het | 85.7607 | 82.4769 | 89.3168 | 89.6940 | 1878 | 399 | 2157 | 258 | 42 | 16.2791 | |
| gduggal-snapvard | INDEL | * | map_l100_m2_e0 | * | 86.0203 | 89.1958 | 83.0632 | 86.5245 | 3294 | 399 | 4561 | 930 | 439 | 47.2043 | |
| qzeng-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 83.9455 | 85.0094 | 82.9080 | 59.5221 | 2257 | 398 | 3216 | 663 | 302 | 45.5505 | |
| mlin-fermikit | INDEL | I1_5 | map_l125_m2_e0 | * | 67.2515 | 53.6756 | 90.0196 | 80.9186 | 460 | 397 | 460 | 51 | 46 | 90.1961 | |
| gduggal-snapfb | SNP | ti | map_l150_m2_e1 | homalt | 97.2023 | 94.8395 | 99.6858 | 79.8530 | 7296 | 397 | 7297 | 23 | 14 | 60.8696 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 18.3861 | 14.4397 | 25.3012 | 64.2755 | 67 | 397 | 63 | 186 | 4 | 2.1505 | |
| ghariani-varprowl | SNP | ti | map_siren | het | 98.6913 | 99.3636 | 98.0280 | 62.9270 | 61985 | 397 | 61987 | 1247 | 191 | 15.3168 | |
| cchapple-custom | INDEL | D1_5 | HG002complexvar | * | 99.2131 | 98.7865 | 99.6433 | 53.2355 | 32318 | 397 | 31288 | 112 | 96 | 85.7143 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.8615 | 94.2539 | 99.6175 | 50.6158 | 6512 | 397 | 6511 | 25 | 20 | 80.0000 | |
| gduggal-bwaplat | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 86.8721 | 77.5325 | 98.7699 | 72.5739 | 1370 | 397 | 1365 | 17 | 15 | 88.2353 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 86.9339 | 77.1098 | 99.6266 | 47.5519 | 1334 | 396 | 1334 | 5 | 2 | 40.0000 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 88.0582 | 79.0032 | 99.4576 | 57.3453 | 1490 | 396 | 1467 | 8 | 7 | 87.5000 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 47.4256 | 81.8182 | 33.3900 | 61.2010 | 1782 | 396 | 1769 | 3529 | 3376 | 95.6645 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 46.1659 | 40.4511 | 53.7611 | 64.5212 | 269 | 396 | 243 | 209 | 202 | 96.6507 | |
| gduggal-bwafb | INDEL | D16_PLUS | HG002complexvar | * | 83.1933 | 75.8977 | 92.0405 | 54.5245 | 1247 | 396 | 1272 | 110 | 107 | 97.2727 | |
| ghariani-varprowl | SNP | ti | map_l125_m2_e1 | * | 98.2162 | 98.7046 | 97.7326 | 76.3818 | 30173 | 396 | 30173 | 700 | 158 | 22.5714 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 1.4925 | 0.7519 | 100.0000 | 83.3333 | 3 | 396 | 3 | 0 | 0 | ||
| ghariani-varprowl | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 85.9332 | 98.8085 | 76.0265 | 77.4229 | 32840 | 396 | 32867 | 10364 | 9929 | 95.8028 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 19.2946 | 18.8525 | 19.7581 | 78.5095 | 92 | 396 | 49 | 199 | 5 | 2.5126 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 0.0000 | 19.3483 | 0.0000 | 0.0000 | 95 | 396 | 0 | 0 | 0 | ||
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 88.2045 | 85.6313 | 90.9371 | 50.7128 | 2360 | 396 | 2358 | 235 | 230 | 97.8723 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.4422 | 96.4266 | 98.4794 | 49.9423 | 10686 | 396 | 10686 | 165 | 162 | 98.1818 | |
| rpoplin-dv42 | SNP | * | map_l100_m2_e1 | het | 99.2783 | 99.1577 | 99.3992 | 66.0072 | 46503 | 395 | 46491 | 281 | 142 | 50.5338 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 73.0631 | 58.4648 | 97.3776 | 92.1719 | 556 | 395 | 557 | 15 | 13 | 86.6667 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 17.0622 | 9.6110 | 75.9259 | 78.6561 | 42 | 395 | 41 | 13 | 13 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | * | homalt | 99.1875 | 99.1927 | 99.1824 | 59.4207 | 48531 | 395 | 48522 | 400 | 203 | 50.7500 | |
| egarrison-hhga | INDEL | D1_5 | HG002complexvar | het | 97.8863 | 98.0978 | 97.6758 | 52.4481 | 20370 | 395 | 20424 | 486 | 392 | 80.6584 | |
| jlack-gatk | SNP | tv | * | het | 99.3606 | 99.9332 | 98.7945 | 31.3268 | 591301 | 395 | 591230 | 7214 | 153 | 2.1209 | |
| ghariani-varprowl | SNP | ti | map_l125_m2_e0 | * | 98.2029 | 98.6946 | 97.7160 | 76.3322 | 29863 | 395 | 29863 | 698 | 158 | 22.6361 | |
| gduggal-snapfb | SNP | ti | map_l150_m2_e0 | homalt | 97.1871 | 94.8136 | 99.6825 | 79.8291 | 7221 | 395 | 7222 | 23 | 14 | 60.8696 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 17.0622 | 9.6110 | 75.9259 | 78.6561 | 42 | 395 | 41 | 13 | 13 | 100.0000 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 92.5568 | 89.9466 | 95.3230 | 44.4415 | 3534 | 395 | 3954 | 194 | 181 | 93.2990 | |
| cchapple-custom | SNP | * | map_l150_m1_e0 | homalt | 98.2123 | 96.4961 | 99.9908 | 66.3750 | 10878 | 395 | 10874 | 1 | 1 | 100.0000 | |
| cchapple-custom | SNP | tv | map_siren | het | 97.1514 | 98.6228 | 95.7232 | 66.6384 | 28215 | 394 | 28291 | 1264 | 181 | 14.3196 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 91.8091 | 85.5307 | 99.0822 | 46.3398 | 2329 | 394 | 2375 | 22 | 22 | 100.0000 | |
| gduggal-bwavard | SNP | * | map_l150_m1_e0 | het | 92.8051 | 97.9602 | 88.1654 | 84.8061 | 18922 | 394 | 18699 | 2510 | 124 | 4.9402 | |
| rpoplin-dv42 | INDEL | I1_5 | * | het | 99.3402 | 99.5015 | 99.1794 | 60.2585 | 78647 | 394 | 78679 | 651 | 605 | 92.9339 | |
| gduggal-snapplat | SNP | tv | map_l125_m0_e0 | homalt | 90.2668 | 82.2602 | 100.0000 | 75.6753 | 1827 | 394 | 1828 | 0 | 0 | ||