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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
77701-77750 / 86044 show all | |||||||||||||||
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 93.5967 | 90.2348 | 97.2188 | 50.5577 | 3151 | 341 | 3146 | 90 | 73 | 81.1111 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.0697 | 98.8184 | 99.3222 | 69.4679 | 30775 | 368 | 30774 | 210 | 73 | 34.7619 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.0697 | 98.8184 | 99.3222 | 69.4679 | 30775 | 368 | 30774 | 210 | 73 | 34.7619 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 95.2063 | 96.6159 | 93.8373 | 59.1611 | 1142 | 40 | 1142 | 75 | 73 | 97.3333 | |
| hfeng-pmm3 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.9574 | 97.3744 | 96.5440 | 64.7133 | 2151 | 58 | 2151 | 77 | 74 | 96.1039 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.2031 | 96.0157 | 98.4203 | 68.4990 | 5374 | 223 | 5358 | 86 | 74 | 86.0465 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9752 | 96.7154 | 99.2683 | 46.8913 | 10718 | 364 | 10718 | 79 | 74 | 93.6709 | |
| hfeng-pmm2 | INDEL | D1_5 | * | homalt | 99.8457 | 99.8467 | 99.8447 | 59.0004 | 48851 | 75 | 48855 | 76 | 74 | 97.3684 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 80.8159 | 84.8980 | 77.1084 | 78.5252 | 416 | 74 | 256 | 76 | 74 | 97.3684 | |
| mlin-fermikit | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 82.5569 | 70.6298 | 99.3305 | 60.9945 | 10889 | 4528 | 10979 | 74 | 74 | 100.0000 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 50.0995 | 86.0000 | 35.3448 | 60.4096 | 43 | 7 | 41 | 75 | 74 | 98.6667 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m0_e0 | homalt | 70.9924 | 72.0930 | 69.9248 | 75.4613 | 186 | 72 | 186 | 80 | 74 | 92.5000 | |
| qzeng-custom | SNP | * | HG002compoundhet | homalt | 98.8868 | 98.8963 | 98.8772 | 42.3069 | 10663 | 119 | 8190 | 93 | 74 | 79.5699 | |
| ndellapenna-hhga | INDEL | I6_15 | HG002complexvar | * | 96.1681 | 95.0125 | 97.3521 | 56.1640 | 4553 | 239 | 4559 | 124 | 74 | 59.6774 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.4308 | 99.2074 | 99.6552 | 61.9169 | 28036 | 224 | 28038 | 97 | 74 | 76.2887 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 51.5638 | 41.4948 | 68.0851 | 72.2550 | 161 | 227 | 160 | 75 | 74 | 98.6667 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 67.9363 | 62.1469 | 74.9153 | 66.2471 | 220 | 134 | 221 | 74 | 74 | 100.0000 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 53.8900 | 46.6238 | 63.8393 | 72.5153 | 145 | 166 | 143 | 81 | 74 | 91.3580 | |
| jmaeng-gatk | INDEL | D6_15 | HG002complexvar | * | 97.9225 | 97.3595 | 98.4921 | 58.5358 | 5162 | 140 | 5160 | 79 | 74 | 93.6709 | |
| jmaeng-gatk | INDEL | I1_5 | HG002compoundhet | het | 94.2604 | 97.6471 | 91.1007 | 86.7453 | 830 | 20 | 778 | 76 | 74 | 97.3684 | |
| jpowers-varprowl | INDEL | * | map_l125_m2_e0 | het | 92.9134 | 93.3142 | 92.5160 | 89.8956 | 1298 | 93 | 1298 | 105 | 74 | 70.4762 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.5520 | 95.8237 | 99.3437 | 50.3216 | 16933 | 738 | 16803 | 111 | 74 | 66.6667 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.5520 | 95.8237 | 99.3437 | 50.3216 | 16933 | 738 | 16803 | 111 | 74 | 66.6667 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 97.5125 | 95.6457 | 99.4536 | 45.9819 | 13421 | 611 | 13651 | 75 | 74 | 98.6667 | |
| ghariani-varprowl | INDEL | * | map_l125_m2_e0 | het | 91.3175 | 97.9152 | 85.5528 | 92.0328 | 1362 | 29 | 1362 | 230 | 74 | 32.1739 | |
| ghariani-varprowl | INDEL | I16_PLUS | * | homalt | 77.5054 | 66.3037 | 93.2615 | 54.3852 | 1035 | 526 | 1038 | 75 | 74 | 98.6667 | |
| ghariani-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 73.6476 | 94.3083 | 60.4126 | 87.0492 | 1193 | 72 | 1230 | 806 | 74 | 9.1811 | |
| ghariani-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 89.2684 | 99.7868 | 80.7560 | 85.2172 | 468 | 1 | 470 | 112 | 74 | 66.0714 | |
| ghariani-varprowl | SNP | tv | map_l150_m1_e0 | het | 96.2185 | 98.9058 | 93.6733 | 82.5202 | 6870 | 76 | 6870 | 464 | 74 | 15.9483 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 58.8714 | 87.8468 | 44.2696 | 89.1685 | 1330 | 184 | 1294 | 1629 | 74 | 4.5427 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 87.0072 | 98.9272 | 77.6508 | 87.8604 | 3873 | 42 | 3874 | 1115 | 74 | 6.6368 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 13.8244 | 10.6122 | 19.8251 | 85.5882 | 52 | 438 | 68 | 275 | 74 | 26.9091 | |
| gduggal-bwavard | INDEL | * | map_l125_m2_e0 | * | 91.5832 | 95.0364 | 88.3721 | 90.1236 | 2087 | 109 | 2090 | 275 | 74 | 26.9091 | |
| gduggal-bwavard | SNP | tv | map_l125_m2_e1 | * | 95.0540 | 97.9288 | 92.3431 | 80.3827 | 16312 | 345 | 16257 | 1348 | 74 | 5.4896 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 92.5726 | 90.3810 | 94.8730 | 43.3628 | 1945 | 207 | 1943 | 105 | 74 | 70.4762 | |
| gduggal-bwafb | INDEL | D1_5 | HG002compoundhet | het | 94.6747 | 91.3773 | 98.2190 | 47.8412 | 1579 | 149 | 7831 | 142 | 74 | 52.1127 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 62.5592 | 92.9577 | 47.1429 | 58.2090 | 66 | 5 | 66 | 74 | 74 | 100.0000 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 89.0456 | 96.0304 | 83.0080 | 88.0462 | 2274 | 94 | 2296 | 470 | 74 | 15.7447 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 6.0167 | 3.3981 | 26.2295 | 42.4528 | 7 | 199 | 32 | 90 | 74 | 82.2222 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.7863 | 96.9500 | 96.6233 | 75.9515 | 2384 | 75 | 2375 | 83 | 74 | 89.1566 | |
| rpoplin-dv42 | SNP | ti | map_l125_m1_e0 | het | 99.1441 | 98.9434 | 99.3457 | 70.2153 | 18073 | 193 | 18069 | 119 | 74 | 62.1849 | |
| rpoplin-dv42 | SNP | ti | map_l125_m2_e0 | het | 99.1665 | 98.9669 | 99.3669 | 71.7774 | 18681 | 195 | 18677 | 119 | 74 | 62.1849 | |
| rpoplin-dv42 | SNP | ti | map_l125_m2_e1 | het | 99.1705 | 98.9679 | 99.3738 | 71.8144 | 18890 | 197 | 18886 | 119 | 74 | 62.1849 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 91.5664 | 93.9498 | 89.3010 | 79.9025 | 823 | 53 | 626 | 75 | 74 | 98.6667 | |
| raldana-dualsentieon | INDEL | I1_5 | HG002compoundhet | het | 88.2507 | 86.4706 | 90.1055 | 86.0431 | 735 | 115 | 683 | 75 | 74 | 98.6667 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 67.4030 | 55.6452 | 85.4610 | 99.7606 | 69 | 55 | 482 | 82 | 74 | 90.2439 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 63.7790 | 63.3136 | 64.2512 | 66.5049 | 107 | 62 | 133 | 74 | 74 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 95.7416 | 95.5607 | 95.9231 | 39.1360 | 4542 | 211 | 4541 | 193 | 74 | 38.3420 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.9522 | 99.9450 | 97.9790 | 62.3287 | 3636 | 2 | 3636 | 75 | 74 | 98.6667 | |
| anovak-vg | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 60.8555 | 82.6087 | 48.1707 | 53.0086 | 76 | 16 | 79 | 85 | 74 | 87.0588 | |