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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
6551-6600 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.8289 | 96.6593 | 96.9990 | 75.1800 | 4832 | 167 | 4816 | 149 | 119 | 79.8658 | |
| raldana-dualsentieon | INDEL | * | HG002complexvar | homalt | 99.7249 | 99.9038 | 99.5467 | 56.9673 | 27001 | 26 | 27010 | 123 | 119 | 96.7480 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 84.4639 | 91.8699 | 78.1629 | 66.9151 | 452 | 40 | 451 | 126 | 119 | 94.4444 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 84.5227 | 93.4426 | 77.1574 | 75.5280 | 456 | 32 | 456 | 135 | 119 | 88.1481 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m2_e1 | homalt | 79.7254 | 79.6774 | 79.7735 | 78.1084 | 494 | 126 | 493 | 125 | 119 | 95.2000 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 65.0860 | 56.7347 | 76.3203 | 57.3091 | 417 | 318 | 448 | 139 | 119 | 85.6115 | |
| ndellapenna-hhga | SNP | ti | HG002compoundhet | homalt | 98.8916 | 99.5266 | 98.2646 | 31.2248 | 7359 | 35 | 7361 | 130 | 119 | 91.5385 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 87.8478 | 91.5179 | 84.4608 | 66.3644 | 1640 | 152 | 1723 | 317 | 119 | 37.5394 | |
| anovak-vg | INDEL | D1_5 | map_l100_m1_e0 | * | 84.4511 | 85.4978 | 83.4298 | 83.8652 | 1580 | 268 | 1586 | 315 | 119 | 37.7778 | |
| cchapple-custom | SNP | * | map_l150_m0_e0 | het | 94.9871 | 95.8312 | 94.1577 | 84.6817 | 7609 | 331 | 7607 | 472 | 119 | 25.2119 | |
| cchapple-custom | SNP | ti | map_l125_m0_e0 | het | 95.6528 | 96.1152 | 95.1947 | 80.1979 | 7942 | 321 | 7944 | 401 | 119 | 29.6758 | |
| ckim-dragen | SNP | * | map_l100_m1_e0 | het | 98.1047 | 99.2152 | 97.0189 | 72.1356 | 45003 | 356 | 45009 | 1383 | 119 | 8.6045 | |
| ckim-dragen | SNP | * | map_l100_m2_e0 | het | 98.0933 | 99.2263 | 96.9859 | 73.8971 | 46040 | 359 | 46046 | 1431 | 119 | 8.3159 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 78.4484 | 88.3268 | 70.5573 | 76.2813 | 1362 | 180 | 1342 | 560 | 119 | 21.2500 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 41.1414 | 67.0732 | 29.6703 | 62.4742 | 55 | 27 | 54 | 128 | 119 | 92.9688 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 83.6651 | 85.4732 | 81.9319 | 70.4517 | 1165 | 198 | 1179 | 260 | 119 | 45.7692 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 84.5240 | 82.7851 | 86.3375 | 67.9071 | 755 | 157 | 752 | 119 | 119 | 100.0000 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 54.7324 | 72.4832 | 43.9655 | 65.0075 | 108 | 41 | 102 | 130 | 119 | 91.5385 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 67.0995 | 63.6364 | 70.9612 | 72.1865 | 1372 | 784 | 1410 | 577 | 119 | 20.6239 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 88.7546 | 84.9330 | 92.9364 | 52.1776 | 1522 | 270 | 1592 | 121 | 119 | 98.3471 | |
| eyeh-varpipe | INDEL | I16_PLUS | HG002compoundhet | het | 2.3810 | 4.2553 | 1.6529 | 50.2058 | 2 | 45 | 2 | 119 | 119 | 100.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 31.0297 | 20.4204 | 64.5833 | 56.8123 | 136 | 530 | 217 | 119 | 119 | 100.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 31.0297 | 20.4204 | 64.5833 | 56.8123 | 136 | 530 | 217 | 119 | 119 | 100.0000 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 80.3090 | 93.6464 | 70.2970 | 75.8518 | 339 | 23 | 284 | 120 | 119 | 99.1667 | |
| rpoplin-dv42 | SNP | ti | map_l100_m1_e0 | * | 99.4597 | 99.2844 | 99.6356 | 62.6996 | 47588 | 343 | 47581 | 174 | 118 | 67.8161 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 86.4073 | 86.7056 | 86.1111 | 74.4351 | 1337 | 205 | 1364 | 220 | 118 | 53.6364 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 83.1359 | 92.9012 | 75.2282 | 88.8693 | 1204 | 92 | 1236 | 407 | 118 | 28.9926 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.3901 | 95.8574 | 98.9725 | 68.4554 | 15411 | 666 | 15412 | 160 | 118 | 73.7500 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.3901 | 95.8574 | 98.9725 | 68.4554 | 15411 | 666 | 15412 | 160 | 118 | 73.7500 | |
| jlack-gatk | SNP | ti | map_l150_m2_e1 | het | 94.5873 | 98.9166 | 90.6210 | 86.3363 | 12874 | 141 | 12870 | 1332 | 118 | 8.8589 | |
| gduggal-snapvard | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 83.9078 | 94.1790 | 75.6567 | 81.6542 | 5873 | 363 | 5818 | 1872 | 118 | 6.3034 | |
| gduggal-snapfb | SNP | ti | map_l250_m1_e0 | het | 93.8477 | 95.0809 | 92.6461 | 86.7956 | 2822 | 146 | 2822 | 224 | 118 | 52.6786 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 63.3305 | 56.2021 | 72.5296 | 71.5411 | 367 | 286 | 367 | 139 | 118 | 84.8921 | |
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 65.6871 | 92.0525 | 51.0621 | 85.0059 | 1193 | 103 | 1226 | 1175 | 118 | 10.0426 | |
| ghariani-varprowl | SNP | tv | map_l125_m2_e1 | * | 97.4430 | 98.7213 | 96.1975 | 78.1381 | 16444 | 213 | 16444 | 650 | 118 | 18.1538 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 62.3646 | 92.6829 | 46.9925 | 68.5950 | 38 | 3 | 125 | 141 | 118 | 83.6879 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m1_e0 | homalt | 78.9341 | 78.8851 | 78.9831 | 76.7350 | 467 | 125 | 466 | 124 | 118 | 95.1613 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m2_e0 | homalt | 79.5902 | 79.5417 | 79.6388 | 77.9587 | 486 | 125 | 485 | 124 | 118 | 95.1613 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 50.5670 | 63.6364 | 41.9512 | 31.6667 | 14 | 8 | 86 | 119 | 118 | 99.1597 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 92.4986 | 87.0629 | 98.6582 | 85.3332 | 27114 | 4029 | 27131 | 369 | 118 | 31.9783 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 92.4986 | 87.0629 | 98.6582 | 85.3332 | 27114 | 4029 | 27131 | 369 | 118 | 31.9783 | |
| gduggal-bwaplat | SNP | ti | map_siren | * | 90.8656 | 83.6301 | 99.4716 | 68.7099 | 83927 | 16428 | 83958 | 446 | 118 | 26.4574 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 86.1043 | 94.9187 | 78.7879 | 57.8125 | 467 | 25 | 468 | 126 | 118 | 93.6508 | |
| egarrison-hhga | INDEL | I16_PLUS | HG002compoundhet | * | 86.9177 | 82.7345 | 91.5464 | 49.7800 | 1773 | 370 | 1776 | 164 | 118 | 71.9512 | |
| egarrison-hhga | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 91.8274 | 91.5346 | 92.1220 | 61.6285 | 2022 | 187 | 2023 | 173 | 118 | 68.2081 | |
| ckim-isaac | INDEL | I16_PLUS | HG002compoundhet | het | 19.1083 | 31.9149 | 13.6364 | 72.1014 | 15 | 32 | 21 | 133 | 118 | 88.7218 | |
| ckim-isaac | INDEL | I6_15 | HG002compoundhet | homalt | 15.7021 | 38.7097 | 9.8485 | 69.8630 | 12 | 19 | 13 | 119 | 118 | 99.1597 | |
| ckim-vqsr | INDEL | D1_5 | * | het | 99.6940 | 99.6963 | 99.6917 | 60.8657 | 87308 | 266 | 87313 | 270 | 118 | 43.7037 | |
| ciseli-custom | INDEL | I1_5 | map_l100_m0_e0 | * | 58.4054 | 52.3020 | 66.1215 | 87.8959 | 284 | 259 | 283 | 145 | 118 | 81.3793 | |
| ciseli-custom | SNP | ti | map_siren | het | 88.8574 | 85.8902 | 92.0370 | 60.6835 | 53580 | 8802 | 53468 | 4626 | 118 | 2.5508 | |