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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1351-1400 / 86044 show all | |||||||||||||||
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 61.9377 | 88.6347 | 47.6003 | 71.2150 | 1201 | 154 | 1210 | 1332 | 1313 | 98.5736 | |
| anovak-vg | SNP | tv | map_l100_m1_e0 | * | 83.4211 | 89.3066 | 78.2634 | 70.1430 | 21881 | 2620 | 21848 | 6068 | 1313 | 21.6381 | |
| mlin-fermikit | SNP | * | HG002compoundhet | homalt | 92.6523 | 98.4233 | 87.5206 | 41.6338 | 10612 | 170 | 10618 | 1514 | 1310 | 86.5258 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 94.4932 | 92.6377 | 96.4246 | 45.4241 | 33898 | 2694 | 37756 | 1400 | 1310 | 93.5714 | |
| gduggal-snapplat | SNP | * | map_siren | het | 96.5899 | 96.2777 | 96.9043 | 72.4626 | 87604 | 3387 | 87710 | 2802 | 1309 | 46.7166 | |
| ndellapenna-hhga | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 81.6855 | 91.2376 | 73.9439 | 67.5049 | 3686 | 354 | 4061 | 1431 | 1308 | 91.4046 | |
| gduggal-snapfb | INDEL | D1_5 | * | homalt | 97.4626 | 98.4998 | 96.4470 | 62.9841 | 48192 | 734 | 48237 | 1777 | 1307 | 73.5509 | |
| jpowers-varprowl | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 81.7040 | 72.4326 | 93.6973 | 66.4963 | 22281 | 8480 | 22240 | 1496 | 1307 | 87.3663 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 40.0753 | 30.3227 | 59.0755 | 67.9189 | 1917 | 4405 | 1917 | 1328 | 1307 | 98.4187 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 40.0753 | 30.3227 | 59.0755 | 67.9189 | 1917 | 4405 | 1917 | 1328 | 1307 | 98.4187 | |
| jpowers-varprowl | SNP | ti | * | * | 99.5767 | 99.5483 | 99.6052 | 21.1558 | 2076086 | 9421 | 2076295 | 8230 | 1307 | 15.8809 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.1122 | 95.6040 | 96.6259 | 60.2914 | 41430 | 1905 | 41238 | 1440 | 1303 | 90.4861 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 71.3299 | 69.4719 | 73.2899 | 58.1798 | 3302 | 1451 | 4725 | 1722 | 1302 | 75.6098 | |
| mlin-fermikit | INDEL | * | HG002complexvar | het | 95.8810 | 94.8801 | 96.9032 | 52.4432 | 43846 | 2366 | 43401 | 1387 | 1299 | 93.6554 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.2804 | 95.7563 | 96.8102 | 77.5473 | 41496 | 1839 | 41428 | 1365 | 1297 | 95.0183 | |
| gduggal-bwafb | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 96.5493 | 97.3408 | 95.7705 | 73.5567 | 29943 | 818 | 29935 | 1322 | 1296 | 98.0333 | |
| anovak-vg | SNP | ti | map_l150_m1_e0 | het | 75.5864 | 89.6281 | 65.3485 | 80.5450 | 11087 | 1283 | 11006 | 5836 | 1295 | 22.1899 | |
| qzeng-custom | INDEL | * | HG002compoundhet | homalt | 47.3681 | 97.3761 | 31.2960 | 66.5488 | 668 | 18 | 681 | 1495 | 1295 | 86.6221 | |
| qzeng-custom | INDEL | D1_5 | * | * | 98.2982 | 97.8575 | 98.7428 | 57.2067 | 143601 | 3144 | 144677 | 1842 | 1294 | 70.2497 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 79.1914 | 73.9716 | 85.2037 | 51.7929 | 13181 | 4638 | 24318 | 4223 | 1294 | 30.6417 | |
| ghariani-varprowl | SNP | ti | * | * | 99.5372 | 99.8784 | 99.1982 | 22.5770 | 2082957 | 2536 | 2083186 | 16837 | 1291 | 7.6676 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 45.2624 | 94.5183 | 29.7558 | 27.9326 | 569 | 33 | 585 | 1381 | 1290 | 93.4106 | |
| eyeh-varpipe | INDEL | I6_15 | * | het | 83.0781 | 80.3150 | 86.0381 | 40.9246 | 8058 | 1975 | 8048 | 1306 | 1290 | 98.7749 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 44.1195 | 41.2053 | 47.4772 | 55.2735 | 1094 | 1561 | 1355 | 1499 | 1289 | 85.9907 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 44.8723 | 35.0206 | 62.4365 | 72.5902 | 2214 | 4108 | 2214 | 1332 | 1288 | 96.6967 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 44.8723 | 35.0206 | 62.4365 | 72.5902 | 2214 | 4108 | 2214 | 1332 | 1288 | 96.6967 | |
| gduggal-snapfb | SNP | ti | * | * | 99.4335 | 99.8078 | 99.0620 | 21.3991 | 2081510 | 4008 | 2082093 | 19715 | 1288 | 6.5331 | |
| eyeh-varpipe | INDEL | * | HG002complexvar | het | 95.5256 | 94.2569 | 96.8290 | 49.4429 | 43558 | 2654 | 42048 | 1377 | 1284 | 93.2462 | |
| ciseli-custom | INDEL | I1_5 | HG002complexvar | homalt | 88.0614 | 87.4926 | 88.6376 | 45.0592 | 11766 | 1682 | 11522 | 1477 | 1282 | 86.7976 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 47.7873 | 41.5540 | 56.2207 | 53.8295 | 1690 | 2377 | 1681 | 1309 | 1280 | 97.7846 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 77.5159 | 76.4592 | 78.6021 | 48.9675 | 5148 | 1585 | 5128 | 1396 | 1280 | 91.6905 | |
| anovak-vg | SNP | tv | map_l100_m2_e1 | het | 80.1681 | 92.4332 | 70.7766 | 74.1911 | 14732 | 1206 | 14718 | 6077 | 1278 | 21.0301 | |
| gduggal-bwavard | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 83.0702 | 98.1137 | 72.0266 | 52.1291 | 3589 | 69 | 3579 | 1390 | 1276 | 91.7986 | |
| anovak-vg | SNP | tv | map_l100_m2_e0 | het | 80.0810 | 92.3877 | 70.6676 | 74.1753 | 14576 | 1201 | 14566 | 6046 | 1273 | 21.0552 | |
| anovak-vg | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 44.1057 | 39.2068 | 50.4037 | 54.9961 | 1562 | 2422 | 1748 | 1720 | 1273 | 74.0116 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 70.3858 | 62.2960 | 80.8903 | 55.0300 | 6452 | 3905 | 7814 | 1846 | 1272 | 68.9057 | |
| ghariani-varprowl | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 81.5331 | 72.3481 | 93.3894 | 66.7128 | 22255 | 8506 | 22222 | 1573 | 1272 | 80.8646 | |
| anovak-vg | INDEL | I6_15 | HG002complexvar | * | 48.0486 | 41.4858 | 57.0779 | 45.2877 | 1988 | 2804 | 2008 | 1510 | 1270 | 84.1060 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.7595 | 95.2166 | 96.3087 | 53.9807 | 36089 | 1813 | 35901 | 1376 | 1269 | 92.2238 | |
| anovak-vg | SNP | tv | map_l100_m1_e0 | het | 79.8335 | 92.3396 | 70.3109 | 72.6600 | 14236 | 1181 | 14226 | 6007 | 1268 | 21.1087 | |
| mlin-fermikit | INDEL | * | HG002complexvar | homalt | 95.7600 | 96.3222 | 95.2043 | 55.1307 | 26033 | 994 | 25927 | 1306 | 1267 | 97.0138 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 88.6139 | 96.1944 | 82.1409 | 64.2130 | 5384 | 213 | 6062 | 1318 | 1266 | 96.0546 | |
| gduggal-bwavard | INDEL | I16_PLUS | HG002compoundhet | * | 2.2297 | 1.8199 | 2.8777 | 49.0469 | 39 | 2104 | 40 | 1350 | 1263 | 93.5556 | |
| gduggal-snapfb | INDEL | * | HG002complexvar | het | 90.2528 | 87.9122 | 92.7215 | 54.1807 | 40626 | 5586 | 43300 | 3399 | 1261 | 37.0991 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 77.9762 | 81.6286 | 74.6367 | 40.5656 | 3328 | 749 | 4314 | 1466 | 1261 | 86.0164 | |
| gduggal-bwavard | INDEL | D1_5 | HG002complexvar | * | 93.5349 | 92.9971 | 94.0789 | 54.5678 | 30424 | 2291 | 28886 | 1818 | 1258 | 69.1969 | |
| ciseli-custom | INDEL | D6_15 | HG002complexvar | * | 60.6154 | 60.3471 | 60.8861 | 55.7398 | 3199 | 2102 | 3202 | 2057 | 1257 | 61.1084 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 47.6114 | 41.5540 | 55.7361 | 61.7356 | 1690 | 2377 | 1681 | 1335 | 1256 | 94.0824 | |
| ciseli-custom | INDEL | D1_5 | HG002compoundhet | het | 30.2760 | 33.1981 | 27.8267 | 77.5472 | 573 | 1153 | 1105 | 2866 | 1255 | 43.7893 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 93.0148 | 97.6827 | 88.7726 | 47.1861 | 10117 | 240 | 10097 | 1277 | 1255 | 98.2772 | |