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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
43401-43450 / 86044 show all | |||||||||||||||
| mlin-fermikit | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 88.3886 | 90.9836 | 85.9375 | 59.6215 | 111 | 11 | 110 | 18 | 18 | 100.0000 | |
| mlin-fermikit | INDEL | * | map_l125_m2_e0 | * | 69.1050 | 57.7869 | 85.9364 | 82.6204 | 1269 | 927 | 1271 | 208 | 160 | 76.9231 | |
| mlin-fermikit | INDEL | D1_5 | map_l125_m1_e0 | * | 69.1865 | 57.9044 | 85.9290 | 78.9897 | 630 | 458 | 629 | 103 | 90 | 87.3786 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 90.0260 | 94.5355 | 85.9272 | 79.6359 | 519 | 30 | 519 | 85 | 85 | 100.0000 | |
| jlack-gatk | SNP | tv | map_l150_m1_e0 | het | 91.9297 | 98.8339 | 85.9271 | 86.1869 | 6865 | 81 | 6863 | 1124 | 59 | 5.2491 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 71.5265 | 61.2613 | 85.9244 | 78.5005 | 408 | 258 | 409 | 67 | 27 | 40.2985 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 71.5265 | 61.2613 | 85.9244 | 78.5005 | 408 | 258 | 409 | 67 | 27 | 40.2985 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 82.9932 | 80.2632 | 85.9155 | 91.4458 | 122 | 30 | 122 | 20 | 5 | 25.0000 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 62.5395 | 49.1632 | 85.9155 | 86.2802 | 235 | 243 | 244 | 40 | 7 | 17.5000 | |
| gduggal-snapvard | SNP | ti | map_l100_m0_e0 | het | 90.6971 | 96.0523 | 85.9075 | 80.2123 | 13431 | 552 | 13338 | 2188 | 175 | 7.9982 | |
| ciseli-custom | SNP | * | map_l125_m2_e0 | * | 81.1188 | 76.8380 | 85.9047 | 77.6345 | 35901 | 10822 | 35830 | 5879 | 1516 | 25.7867 | |
| gduggal-snapvard | SNP | * | tech_badpromoters | het | 86.4516 | 87.0130 | 85.8974 | 57.3770 | 67 | 10 | 67 | 11 | 2 | 18.1818 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 91.8644 | 98.7250 | 85.8954 | 82.3891 | 542 | 7 | 542 | 89 | 85 | 95.5056 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 78.5618 | 72.3842 | 85.8922 | 52.6470 | 10702 | 4083 | 10825 | 1778 | 1586 | 89.2013 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 87.6321 | 89.4447 | 85.8915 | 75.4124 | 1627 | 192 | 1869 | 307 | 263 | 85.6678 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 87.6321 | 89.4447 | 85.8915 | 75.4124 | 1627 | 192 | 1869 | 307 | 263 | 85.6678 | |
| jlack-gatk | SNP | tv | map_l100_m0_e0 | het | 91.9563 | 98.9477 | 85.8877 | 83.2329 | 7146 | 76 | 7145 | 1174 | 61 | 5.1959 | |
| mlin-fermikit | INDEL | I1_5 | map_l100_m2_e1 | homalt | 74.9478 | 66.4815 | 85.8852 | 77.4663 | 359 | 181 | 359 | 59 | 57 | 96.6102 | |
| ndellapenna-hhga | INDEL | D16_PLUS | map_l100_m1_e0 | * | 83.6913 | 81.6092 | 85.8824 | 87.5549 | 71 | 16 | 73 | 12 | 6 | 50.0000 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 70.5314 | 59.8361 | 85.8824 | 65.4472 | 73 | 49 | 73 | 12 | 12 | 100.0000 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 88.7047 | 91.7202 | 85.8812 | 83.6926 | 2426 | 219 | 2573 | 423 | 179 | 42.3168 | |
| gduggal-bwavard | SNP | tv | map_l100_m0_e0 | het | 91.6040 | 98.1446 | 85.8808 | 81.9878 | 7088 | 134 | 7074 | 1163 | 45 | 3.8693 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 75.9096 | 68.0162 | 85.8757 | 72.5581 | 168 | 79 | 152 | 25 | 16 | 64.0000 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 56.0755 | 41.6302 | 85.8726 | 84.0433 | 2472 | 3466 | 2480 | 408 | 341 | 83.5784 | |
| raldana-dualsentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 82.1683 | 78.7720 | 85.8708 | 53.3827 | 1655 | 446 | 1568 | 258 | 253 | 98.0620 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 87.2686 | 88.7234 | 85.8607 | 64.7399 | 417 | 53 | 419 | 69 | 36 | 52.1739 | |
| jlack-gatk | INDEL | * | map_l150_m0_e0 | * | 91.3832 | 97.6654 | 85.8603 | 94.2048 | 502 | 12 | 504 | 83 | 3 | 3.6145 | |
| mlin-fermikit | INDEL | I1_5 | map_l100_m2_e0 | homalt | 74.8140 | 66.2900 | 85.8537 | 77.2601 | 352 | 179 | 352 | 58 | 56 | 96.5517 | |
| jmaeng-gatk | INDEL | * | map_l250_m1_e0 | het | 90.5473 | 95.7895 | 85.8491 | 97.7177 | 182 | 8 | 182 | 30 | 2 | 6.6667 | |
| qzeng-custom | INDEL | * | map_l250_m2_e1 | het | 76.6254 | 69.1943 | 85.8447 | 98.2768 | 146 | 65 | 188 | 31 | 16 | 51.6129 | |
| ghariani-varprowl | INDEL | D1_5 | map_l125_m0_e0 | * | 90.8918 | 96.5726 | 85.8423 | 90.8419 | 479 | 17 | 479 | 79 | 10 | 12.6582 | |
| jlack-gatk | INDEL | D6_15 | map_l100_m0_e0 | * | 89.8148 | 94.1748 | 85.8407 | 90.7453 | 97 | 6 | 97 | 16 | 2 | 12.5000 | |
| mlin-fermikit | INDEL | D6_15 | map_siren | * | 81.1872 | 77.0138 | 85.8388 | 82.0071 | 392 | 117 | 394 | 65 | 53 | 81.5385 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 86.6705 | 87.5205 | 85.8369 | 72.0400 | 533 | 76 | 600 | 99 | 82 | 82.8283 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 87.2533 | 88.7226 | 85.8319 | 38.8447 | 9189 | 1168 | 9178 | 1515 | 1403 | 92.6073 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 52.7266 | 38.0507 | 85.8309 | 70.4516 | 6106 | 9941 | 5785 | 955 | 426 | 44.6073 | |
| ghariani-varprowl | INDEL | D16_PLUS | HG002complexvar | homalt | 80.0982 | 75.0865 | 85.8268 | 71.4927 | 217 | 72 | 218 | 36 | 33 | 91.6667 | |
| jpowers-varprowl | INDEL | D16_PLUS | HG002complexvar | homalt | 80.0982 | 75.0865 | 85.8268 | 71.4607 | 217 | 72 | 218 | 36 | 33 | 91.6667 | |
| gduggal-bwavard | INDEL | * | map_l150_m1_e0 | * | 90.3416 | 95.3662 | 85.8199 | 91.3779 | 1276 | 62 | 1277 | 211 | 47 | 22.2749 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 78.2874 | 71.9726 | 85.8170 | 51.6431 | 7976 | 3106 | 8120 | 1342 | 1151 | 85.7675 | |
| jmaeng-gatk | INDEL | D1_5 | map_l250_m2_e1 | het | 92.0152 | 99.1803 | 85.8156 | 97.4396 | 121 | 1 | 121 | 20 | 1 | 5.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 72.9935 | 63.5053 | 85.8149 | 62.8966 | 837 | 481 | 853 | 141 | 132 | 93.6170 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 91.8329 | 98.7645 | 85.8105 | 79.7572 | 5356 | 67 | 5352 | 885 | 251 | 28.3616 | |
| ciseli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 91.8329 | 98.7645 | 85.8105 | 79.7572 | 5356 | 67 | 5352 | 885 | 251 | 28.3616 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 83.2380 | 80.8271 | 85.7971 | 78.5980 | 215 | 51 | 296 | 49 | 48 | 97.9592 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 89.6142 | 93.7888 | 85.7955 | 36.9176 | 151 | 10 | 151 | 25 | 25 | 100.0000 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 89.8295 | 94.2654 | 85.7923 | 82.5729 | 1726 | 105 | 1727 | 286 | 3 | 1.0490 | |
| ciseli-custom | INDEL | D1_5 | HG002complexvar | het | 87.0231 | 88.2917 | 85.7906 | 58.0288 | 18332 | 2431 | 18318 | 3034 | 650 | 21.4239 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 56.6114 | 42.2485 | 85.7701 | 63.4733 | 1537 | 2101 | 1537 | 255 | 235 | 92.1569 | |
| hfeng-pmm1 | INDEL | D6_15 | HG002compoundhet | het | 82.2937 | 79.0888 | 85.7692 | 65.6236 | 677 | 179 | 669 | 111 | 108 | 97.2973 | |