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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
20051-20100 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.8166 | 98.1371 | 99.5056 | 55.0392 | 19492 | 370 | 19523 | 97 | 32 | 32.9897 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 82.5065 | 98.1366 | 71.1712 | 37.2881 | 158 | 3 | 158 | 64 | 64 | 100.0000 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 80.4071 | 98.1366 | 68.1034 | 35.1955 | 158 | 3 | 158 | 74 | 67 | 90.5405 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9153 | 98.1365 | 99.7066 | 60.6969 | 10901 | 207 | 10875 | 32 | 10 | 31.2500 | |
| jli-custom | SNP | ti | map_l125_m0_e0 | het | 98.6256 | 98.1363 | 99.1199 | 71.4709 | 8109 | 154 | 8109 | 72 | 25 | 34.7222 | |
| hfeng-pmm3 | INDEL | I6_15 | * | het | 98.8597 | 98.1362 | 99.5939 | 56.2294 | 9846 | 187 | 9811 | 40 | 29 | 72.5000 | |
| raldana-dualsentieon | SNP | ti | map_l150_m0_e0 | het | 97.9052 | 98.1362 | 97.6753 | 80.7049 | 5002 | 95 | 5000 | 119 | 1 | 0.8403 | |
| qzeng-custom | INDEL | I1_5 | HG002complexvar | het | 98.6121 | 98.1362 | 99.0926 | 55.1360 | 17850 | 339 | 18675 | 171 | 70 | 40.9357 | |
| gduggal-bwavard | SNP | tv | map_l150_m0_e0 | het | 87.7034 | 98.1358 | 79.2759 | 87.9471 | 2790 | 53 | 2781 | 727 | 17 | 2.3384 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 98.9430 | 98.1340 | 99.7654 | 46.0565 | 3734 | 71 | 3828 | 9 | 9 | 100.0000 | |
| gduggal-bwaplat | SNP | * | * | het | 98.8209 | 98.1336 | 99.5179 | 30.8495 | 1838619 | 34968 | 1839500 | 8912 | 1113 | 12.4888 | |
| hfeng-pmm2 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.8203 | 98.1335 | 99.5168 | 73.5903 | 47370 | 901 | 47163 | 229 | 165 | 72.0524 | |
| gduggal-bwafb | SNP | ti | map_l250_m1_e0 | homalt | 98.9956 | 98.1332 | 99.8733 | 88.0983 | 1577 | 30 | 1577 | 2 | 2 | 100.0000 | |
| jmaeng-gatk | INDEL | * | map_l125_m2_e0 | * | 96.6195 | 98.1330 | 95.1520 | 91.4584 | 2155 | 41 | 2159 | 110 | 11 | 10.0000 | |
| jpowers-varprowl | SNP | * | map_l100_m0_e0 | homalt | 98.9071 | 98.1325 | 99.6940 | 66.9212 | 11403 | 217 | 11403 | 35 | 22 | 62.8571 | |
| gduggal-bwafb | SNP | * | map_l250_m1_e0 | homalt | 98.9560 | 98.1324 | 99.7936 | 88.2570 | 2417 | 46 | 2417 | 5 | 5 | 100.0000 | |
| jli-custom | INDEL | * | map_l150_m1_e0 | * | 98.3164 | 98.1315 | 98.5019 | 88.5230 | 1313 | 25 | 1315 | 20 | 7 | 35.0000 | |
| jlack-gatk | INDEL | * | map_l125_m2_e0 | het | 92.6228 | 98.1308 | 87.7002 | 91.9195 | 1365 | 26 | 1369 | 192 | 9 | 4.6875 | |
| asubramanian-gatk | INDEL | * | func_cds | het | 98.5959 | 98.1308 | 99.0654 | 61.0909 | 210 | 4 | 212 | 2 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D6_15 | HG002compoundhet | het | 89.1342 | 98.1308 | 81.6487 | 68.8379 | 840 | 16 | 832 | 187 | 185 | 98.9305 | |
| gduggal-bwafb | SNP | tv | map_l250_m1_e0 | homalt | 98.8817 | 98.1308 | 99.6441 | 88.5431 | 840 | 16 | 840 | 3 | 3 | 100.0000 | |
| jmaeng-gatk | INDEL | * | map_l125_m2_e0 | het | 95.4980 | 98.1308 | 93.0027 | 92.6879 | 1365 | 26 | 1369 | 103 | 7 | 6.7961 | |
| qzeng-custom | INDEL | * | func_cds | het | 93.8897 | 98.1308 | 90.0000 | 52.8689 | 210 | 4 | 207 | 23 | 2 | 8.6957 | |
| mlin-fermikit | SNP | tv | * | * | 98.7665 | 98.1308 | 99.4104 | 19.3147 | 951572 | 18126 | 951506 | 5643 | 4116 | 72.9399 | |
| rpoplin-dv42 | INDEL | * | func_cds | het | 98.5959 | 98.1308 | 99.0654 | 47.2906 | 210 | 4 | 212 | 2 | 2 | 100.0000 | |
| raldana-dualsentieon | INDEL | * | func_cds | het | 98.5959 | 98.1308 | 99.0654 | 45.9596 | 210 | 4 | 212 | 2 | 0 | 0.0000 | |
| gduggal-bwavard | SNP | tv | map_l100_m2_e1 | het | 94.4719 | 98.1303 | 91.0764 | 80.3818 | 15640 | 298 | 15585 | 1527 | 90 | 5.8939 | |
| cchapple-custom | INDEL | D1_5 | map_siren | * | 97.4907 | 98.1298 | 96.8600 | 78.7253 | 3463 | 66 | 3424 | 111 | 14 | 12.6126 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.6425 | 98.1293 | 99.1611 | 76.9773 | 2413 | 46 | 2364 | 20 | 11 | 55.0000 | |
| gduggal-snapfb | SNP | ti | HG002compoundhet | * | 85.8670 | 98.1291 | 76.3290 | 43.9481 | 17151 | 327 | 17345 | 5379 | 340 | 6.3209 | |
| jmaeng-gatk | INDEL | * | map_l150_m2_e0 | homalt | 98.6416 | 98.1289 | 99.1597 | 89.6206 | 472 | 9 | 472 | 4 | 3 | 75.0000 | |
| ckim-dragen | INDEL | * | map_l150_m2_e0 | homalt | 98.5364 | 98.1289 | 98.9474 | 89.1453 | 472 | 9 | 470 | 5 | 4 | 80.0000 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 99.0555 | 98.1287 | 100.0000 | 47.6606 | 839 | 16 | 839 | 0 | 0 | ||
| hfeng-pmm1 | SNP | * | map_l250_m1_e0 | het | 98.4804 | 98.1283 | 98.8350 | 88.4918 | 4666 | 89 | 4666 | 55 | 10 | 18.1818 | |
| ghariani-varprowl | SNP | * | map_l150_m1_e0 | homalt | 98.8738 | 98.1283 | 99.6307 | 72.3027 | 11062 | 211 | 11062 | 41 | 25 | 60.9756 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.8632 | 98.1277 | 99.6099 | 65.9765 | 3826 | 73 | 3830 | 15 | 10 | 66.6667 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 98.2635 | 98.1273 | 98.4000 | 38.2934 | 262 | 5 | 861 | 14 | 8 | 57.1429 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 95.9707 | 98.1273 | 93.9068 | 59.2105 | 262 | 5 | 262 | 17 | 17 | 100.0000 | |
| hfeng-pmm3 | INDEL | * | map_l125_m1_e0 | het | 98.2769 | 98.1273 | 98.4270 | 85.5800 | 1310 | 25 | 1314 | 21 | 3 | 14.2857 | |
| jlack-gatk | INDEL | * | map_l125_m1_e0 | het | 92.6306 | 98.1273 | 87.7170 | 91.3380 | 1310 | 25 | 1314 | 184 | 8 | 4.3478 | |
| jmaeng-gatk | INDEL | * | map_l125_m1_e0 | het | 95.4569 | 98.1273 | 92.9279 | 92.1545 | 1310 | 25 | 1314 | 100 | 7 | 7.0000 | |
| gduggal-bwavard | INDEL | * | map_l125_m0_e0 | het | 86.9907 | 98.1261 | 78.1250 | 92.7637 | 576 | 11 | 575 | 161 | 28 | 17.3913 | |
| ltrigg-rtg2 | SNP | tv | map_l125_m2_e0 | * | 98.9542 | 98.1260 | 99.7965 | 61.0321 | 16180 | 309 | 16180 | 33 | 5 | 15.1515 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.6704 | 98.1255 | 97.2195 | 71.9856 | 32613 | 623 | 41783 | 1195 | 869 | 72.7197 | |
| jpowers-varprowl | SNP | tv | map_l150_m1_e0 | homalt | 98.7251 | 98.1247 | 99.3330 | 75.8368 | 3872 | 74 | 3872 | 26 | 16 | 61.5385 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 99.0534 | 98.1246 | 100.0000 | 31.5937 | 1465 | 28 | 1468 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 99.0140 | 98.1239 | 99.9205 | 31.1473 | 5021 | 96 | 5025 | 4 | 4 | 100.0000 | |
| hfeng-pmm3 | INDEL | * | map_l150_m2_e1 | * | 98.1943 | 98.1237 | 98.2651 | 88.7746 | 1412 | 27 | 1416 | 25 | 6 | 24.0000 | |
| jlack-gatk | INDEL | * | map_l150_m2_e0 | het | 91.3052 | 98.1236 | 85.3728 | 93.4833 | 889 | 17 | 893 | 153 | 6 | 3.9216 | |
| jmaeng-gatk | INDEL | * | map_l150_m2_e0 | het | 94.5436 | 98.1236 | 91.2155 | 94.1716 | 889 | 17 | 893 | 86 | 6 | 6.9767 | |