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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
3801-3850 / 86044 show all | |||||||||||||||
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.7746 | 96.6611 | 98.9141 | 61.8918 | 63169 | 2182 | 63489 | 697 | 270 | 38.7374 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.7746 | 96.6611 | 98.9141 | 61.8918 | 63169 | 2182 | 63489 | 697 | 270 | 38.7374 | |
| gduggal-bwafb | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.2991 | 99.0593 | 97.5505 | 61.1472 | 27696 | 263 | 27758 | 697 | 164 | 23.5294 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 25.7821 | 22.7376 | 29.7679 | 52.9440 | 299 | 1016 | 295 | 696 | 682 | 97.9885 | |
| gduggal-bwavard | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 43.9869 | 88.4848 | 29.2683 | 52.5554 | 292 | 38 | 288 | 696 | 682 | 97.9885 | |
| ckim-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9696 | 98.6829 | 99.2581 | 73.7654 | 93205 | 1244 | 93112 | 696 | 583 | 83.7644 | |
| cchapple-custom | SNP | tv | map_l125_m2_e1 | * | 96.6306 | 97.3885 | 95.8843 | 75.9688 | 16222 | 435 | 16215 | 696 | 117 | 16.8103 | |
| cchapple-custom | SNP | tv | map_l125_m2_e1 | het | 95.6281 | 97.6500 | 93.6882 | 79.3490 | 10305 | 248 | 10331 | 696 | 117 | 16.8103 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 68.9415 | 78.6340 | 61.3762 | 40.0333 | 449 | 122 | 1106 | 696 | 623 | 89.5115 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 85.8608 | 77.6154 | 96.0663 | 66.4017 | 16997 | 4902 | 16973 | 695 | 593 | 85.3237 | |
| ckim-gatk | INDEL | I1_5 | * | * | 99.3427 | 99.1491 | 99.5371 | 59.3239 | 149382 | 1282 | 149430 | 695 | 401 | 57.6978 | |
| jlack-gatk | SNP | ti | map_l150_m0_e0 | * | 94.8167 | 98.1046 | 91.7420 | 86.3569 | 7712 | 149 | 7710 | 694 | 68 | 9.7983 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 40.5868 | 37.3203 | 44.4800 | 81.8709 | 571 | 959 | 556 | 694 | 384 | 55.3314 | |
| gduggal-bwavard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 40.5868 | 37.3203 | 44.4800 | 81.8709 | 571 | 959 | 556 | 694 | 384 | 55.3314 | |
| ghariani-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 66.4821 | 91.3098 | 52.2696 | 87.6612 | 725 | 69 | 760 | 694 | 0 | 0.0000 | |
| gduggal-snapplat | SNP | tv | map_l125_m2_e1 | * | 93.3986 | 91.2649 | 95.6344 | 83.1005 | 15202 | 1455 | 15203 | 694 | 360 | 51.8732 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 91.0608 | 87.8273 | 94.5415 | 37.6092 | 12107 | 1678 | 12020 | 694 | 633 | 91.2104 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 72.9555 | 67.4217 | 79.4788 | 54.5797 | 2649 | 1280 | 2684 | 693 | 618 | 89.1775 | |
| jpowers-varprowl | INDEL | D1_5 | HG002compoundhet | homalt | 42.6708 | 92.4399 | 27.7372 | 69.2234 | 269 | 22 | 266 | 693 | 591 | 85.2814 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 89.4795 | 84.4436 | 95.1541 | 60.5296 | 13576 | 2501 | 13588 | 692 | 434 | 62.7168 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 89.4795 | 84.4436 | 95.1541 | 60.5296 | 13576 | 2501 | 13588 | 692 | 434 | 62.7168 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 83.7086 | 81.9364 | 85.5593 | 74.2891 | 4096 | 903 | 4100 | 692 | 601 | 86.8497 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 83.7086 | 81.9364 | 85.5593 | 74.2891 | 4096 | 903 | 4100 | 692 | 601 | 86.8497 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 43.4757 | 29.7973 | 80.3688 | 59.6728 | 2837 | 6684 | 2833 | 692 | 587 | 84.8266 | |
| ghariani-varprowl | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 92.2109 | 97.6112 | 87.3769 | 74.0644 | 4740 | 116 | 4790 | 692 | 106 | 15.3179 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 74.4244 | 62.1108 | 92.8275 | 37.1477 | 3631 | 2215 | 8943 | 691 | 673 | 97.3951 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 74.4244 | 62.1108 | 92.8275 | 37.1477 | 3631 | 2215 | 8943 | 691 | 673 | 97.3951 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 88.4778 | 97.5667 | 80.9379 | 76.0931 | 2927 | 73 | 2934 | 691 | 651 | 94.2113 | |
| gduggal-snapplat | INDEL | D6_15 | HG002compoundhet | * | 47.6068 | 33.6951 | 81.0840 | 49.2004 | 3043 | 5988 | 2962 | 691 | 439 | 63.5311 | |
| bgallagher-sentieon | SNP | * | map_siren | het | 99.4455 | 99.6483 | 99.2436 | 58.2943 | 90671 | 320 | 90657 | 691 | 77 | 11.1433 | |
| anovak-vg | INDEL | * | map_l125_m2_e1 | * | 72.6951 | 74.3371 | 71.1241 | 87.8885 | 1654 | 571 | 1702 | 691 | 393 | 56.8741 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.6230 | 97.5440 | 95.7192 | 65.8529 | 14258 | 359 | 15451 | 691 | 402 | 58.1766 | |
| cchapple-custom | SNP | tv | map_l125_m2_e0 | * | 96.6110 | 97.3619 | 95.8717 | 75.9113 | 16054 | 435 | 16047 | 691 | 117 | 16.9320 | |
| cchapple-custom | SNP | tv | map_l125_m2_e0 | het | 95.6050 | 97.6250 | 93.6669 | 79.2937 | 10194 | 248 | 10220 | 691 | 117 | 16.9320 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 91.9346 | 96.5800 | 87.7156 | 44.0577 | 4942 | 175 | 4934 | 691 | 677 | 97.9740 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 94.7847 | 96.0993 | 93.5056 | 43.8048 | 9953 | 404 | 9949 | 691 | 301 | 43.5601 | |
| gduggal-snapplat | SNP | tv | map_l125_m2_e0 | * | 93.3644 | 91.2184 | 95.6138 | 83.0664 | 15041 | 1448 | 15041 | 690 | 359 | 52.0290 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 71.0348 | 99.0643 | 55.3687 | 72.8200 | 847 | 8 | 856 | 690 | 5 | 0.7246 | |
| eyeh-varpipe | SNP | tv | HG002complexvar | het | 99.6993 | 99.8812 | 99.5181 | 20.4147 | 150555 | 179 | 142480 | 690 | 71 | 10.2899 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 57.3083 | 74.2240 | 46.6718 | 65.6383 | 550 | 191 | 603 | 689 | 262 | 38.0261 | |
| ckim-dragen | SNP | ti | map_l125_m2_e1 | het | 97.7431 | 99.0360 | 96.4836 | 78.3312 | 18903 | 184 | 18905 | 689 | 65 | 9.4340 | |
| anovak-vg | INDEL | D16_PLUS | HG002compoundhet | * | 28.7549 | 21.7001 | 42.6065 | 32.2197 | 508 | 1833 | 510 | 687 | 477 | 69.4323 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 53.0813 | 57.1912 | 49.5224 | 53.3105 | 676 | 506 | 674 | 687 | 585 | 85.1528 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 86.3814 | 98.9059 | 76.6723 | 45.1991 | 2260 | 25 | 2258 | 687 | 651 | 94.7598 | |
| gduggal-snapplat | SNP | tv | map_l125_m2_e1 | het | 93.3381 | 93.1962 | 93.4803 | 85.9836 | 9835 | 718 | 9836 | 686 | 353 | 51.4577 | |
| jpowers-varprowl | SNP | * | map_l150_m1_e0 | het | 96.1124 | 95.8014 | 96.4254 | 81.4447 | 18505 | 811 | 18505 | 686 | 205 | 29.8834 | |
| gduggal-snapplat | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 85.4527 | 79.0606 | 92.9693 | 74.0678 | 9039 | 2394 | 9058 | 685 | 58 | 8.4672 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 81.7047 | 98.6709 | 69.7171 | 59.9362 | 1559 | 21 | 1577 | 685 | 12 | 1.7518 | |
| gduggal-snapplat | INDEL | * | map_siren | * | 79.6077 | 71.8219 | 89.2868 | 89.6136 | 5322 | 2088 | 5709 | 685 | 78 | 11.3869 | |
| jlack-gatk | SNP | ti | map_l150_m0_e0 | het | 92.9137 | 98.4304 | 87.9825 | 88.8885 | 5017 | 80 | 5015 | 685 | 60 | 8.7591 | |