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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
5101-5150 / 86044 show all | |||||||||||||||
| ciseli-custom | SNP | tv | map_l150_m1_e0 | homalt | 85.3488 | 82.6913 | 88.1828 | 71.9082 | 3263 | 683 | 3261 | 437 | 339 | 77.5744 | |
| ciseli-custom | INDEL | I16_PLUS | * | homalt | 37.7444 | 29.7886 | 51.4983 | 66.4182 | 465 | 1096 | 464 | 437 | 402 | 91.9908 | |
| ckim-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.7342 | 93.9641 | 95.5170 | 68.9673 | 9465 | 608 | 9311 | 437 | 395 | 90.3890 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 26.7554 | 24.6259 | 29.2880 | 56.6011 | 181 | 554 | 181 | 437 | 436 | 99.7712 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 69.0088 | 62.2563 | 77.4043 | 50.7888 | 1501 | 910 | 1497 | 437 | 418 | 95.6522 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 74.6510 | 71.8045 | 77.7324 | 73.3424 | 1528 | 600 | 1522 | 436 | 398 | 91.2844 | |
| ckim-gatk | INDEL | I1_5 | * | het | 99.5633 | 99.6774 | 99.4495 | 61.8943 | 78786 | 255 | 78766 | 436 | 147 | 33.7156 | |
| jpowers-varprowl | SNP | ti | HG002complexvar | het | 99.4252 | 98.9938 | 99.8603 | 18.1914 | 311597 | 3167 | 311707 | 436 | 90 | 20.6422 | |
| gduggal-bwavard | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.4182 | 95.3879 | 95.4484 | 71.2860 | 9245 | 447 | 9143 | 436 | 182 | 41.7431 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 65.4441 | 60.5202 | 71.2401 | 29.6193 | 1047 | 683 | 1080 | 436 | 388 | 88.9908 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 63.9702 | 49.9564 | 88.9115 | 43.5949 | 3440 | 3446 | 3496 | 436 | 391 | 89.6789 | |
| ghariani-varprowl | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.0759 | 98.6453 | 88.1018 | 77.5526 | 3204 | 44 | 3221 | 435 | 34 | 7.8161 | |
| ghariani-varprowl | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.8554 | 99.9208 | 95.8736 | 65.4859 | 10089 | 8 | 10107 | 435 | 273 | 62.7586 | |
| qzeng-custom | INDEL | * | map_l100_m2_e0 | * | 84.2312 | 79.3934 | 89.6968 | 87.9330 | 2932 | 761 | 3787 | 435 | 68 | 15.6322 | |
| eyeh-varpipe | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 95.1371 | 99.6801 | 90.9901 | 43.0795 | 4674 | 15 | 4393 | 435 | 14 | 3.2184 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 33.7796 | 27.0106 | 45.0758 | 47.5149 | 356 | 962 | 357 | 435 | 415 | 95.4023 | |
| anovak-vg | INDEL | I6_15 | HG002complexvar | het | 40.0214 | 28.2378 | 68.6825 | 52.4803 | 665 | 1690 | 954 | 435 | 281 | 64.5977 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 97.9194 | 98.3001 | 97.5417 | 56.1712 | 16885 | 292 | 17260 | 435 | 173 | 39.7701 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.4310 | 98.7964 | 96.1027 | 79.7737 | 10671 | 130 | 10702 | 434 | 19 | 4.3779 | |
| gduggal-snapfb | SNP | tv | map_l150_m2_e0 | het | 95.8184 | 97.4766 | 94.2156 | 77.2326 | 7069 | 183 | 7069 | 434 | 174 | 40.0922 | |
| gduggal-bwafb | SNP | * | map_l100_m0_e0 | * | 98.7063 | 98.7333 | 98.6792 | 70.9309 | 32425 | 416 | 32426 | 434 | 107 | 24.6544 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 88.5502 | 97.0814 | 81.3973 | 49.1056 | 1896 | 57 | 1899 | 434 | 426 | 98.1567 | |
| qzeng-custom | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9643 | 99.4833 | 98.4507 | 67.9503 | 27535 | 143 | 27515 | 433 | 39 | 9.0069 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.1535 | 96.7800 | 97.5299 | 57.5288 | 17102 | 569 | 17097 | 433 | 414 | 95.6120 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 32.6056 | 25.2495 | 46.0100 | 54.7659 | 253 | 749 | 369 | 433 | 324 | 74.8268 | |
| astatham-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.9849 | 94.4009 | 95.5762 | 69.0899 | 9509 | 564 | 9355 | 433 | 393 | 90.7621 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.1535 | 96.7800 | 97.5299 | 57.5288 | 17102 | 569 | 17097 | 433 | 414 | 95.6120 | |
| ckim-gatk | SNP | * | segdup | het | 98.5246 | 99.5207 | 97.5483 | 94.9213 | 17234 | 83 | 17228 | 433 | 5 | 1.1547 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 77.0060 | 92.0824 | 66.1719 | 76.4316 | 849 | 73 | 847 | 433 | 45 | 10.3926 | |
| ckim-dragen | INDEL | I6_15 | HG002compoundhet | * | 93.2228 | 91.6135 | 94.8896 | 36.8488 | 8040 | 736 | 8040 | 433 | 432 | 99.7691 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 65.5538 | 64.1026 | 67.0722 | 60.4154 | 475 | 266 | 882 | 433 | 97 | 22.4018 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 89.5432 | 89.7781 | 89.3096 | 71.8319 | 3601 | 410 | 3609 | 432 | 17 | 3.9352 | |
| ghariani-varprowl | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.8165 | 99.8119 | 95.8994 | 55.8743 | 10083 | 19 | 10103 | 432 | 262 | 60.6481 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 26.0805 | 23.8095 | 28.8303 | 55.2030 | 175 | 560 | 175 | 432 | 431 | 99.7685 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 48.1230 | 32.2658 | 94.6289 | 66.5252 | 5390 | 11315 | 7611 | 432 | 407 | 94.2130 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 48.1230 | 32.2658 | 94.6289 | 66.5252 | 5390 | 11315 | 7611 | 432 | 407 | 94.2130 | |
| ckim-dragen | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.8109 | 99.7103 | 95.9825 | 45.9159 | 10327 | 30 | 10321 | 432 | 429 | 99.3056 | |
| anovak-vg | SNP | ti | segdup | * | 97.8325 | 97.8809 | 97.7842 | 91.7442 | 19123 | 414 | 19020 | 431 | 163 | 37.8190 | |
| gduggal-snapplat | SNP | * | map_l250_m2_e1 | * | 87.9173 | 82.6718 | 93.8735 | 93.9495 | 6603 | 1384 | 6604 | 431 | 208 | 48.2599 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 94.4491 | 90.7138 | 98.5051 | 60.8883 | 28251 | 2892 | 28401 | 431 | 172 | 39.9072 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 94.4491 | 90.7138 | 98.5051 | 60.8883 | 28251 | 2892 | 28401 | 431 | 172 | 39.9072 | |
| gduggal-bwafb | SNP | ti | map_l100_m1_e0 | * | 99.1029 | 99.1050 | 99.1009 | 66.4175 | 47502 | 429 | 47504 | 431 | 106 | 24.5940 | |
| gduggal-bwavard | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 94.1916 | 95.2534 | 93.1533 | 76.2686 | 5940 | 296 | 5864 | 431 | 178 | 41.2993 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 93.1643 | 88.4244 | 98.4410 | 44.1529 | 12925 | 1692 | 27215 | 431 | 341 | 79.1183 | |
| anovak-vg | INDEL | D1_5 | map_siren | het | 86.2774 | 89.9868 | 82.8617 | 80.2332 | 2049 | 228 | 2079 | 430 | 142 | 33.0233 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.7920 | 99.4303 | 96.2068 | 45.3054 | 10298 | 59 | 10906 | 430 | 320 | 74.4186 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 81.7362 | 74.1234 | 91.0918 | 40.7803 | 4397 | 1535 | 4397 | 430 | 427 | 99.3023 | |
| ndellapenna-hhga | INDEL | D1_5 | HG002complexvar | het | 97.7232 | 97.5199 | 97.9274 | 51.5698 | 20250 | 515 | 20317 | 430 | 365 | 84.8837 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 77.2684 | 79.2312 | 75.4005 | 60.0913 | 1278 | 335 | 1318 | 430 | 259 | 60.2326 | |
| hfeng-pmm3 | SNP | ti | * | het | 99.9388 | 99.9112 | 99.9664 | 17.2454 | 1280753 | 1138 | 1280703 | 430 | 18 | 4.1861 | |