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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
61201-61250 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | C16_PLUS | segdup | het | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| ckim-vqsr | INDEL | * | * | * | 99.2541 | 99.0614 | 99.4476 | 60.7768 | 341308 | 3234 | 341167 | 1895 | 1532 | 80.8443 | |
| ckim-vqsr | INDEL | * | * | het | 99.5204 | 99.5086 | 99.5323 | 62.3713 | 193179 | 954 | 192796 | 906 | 561 | 61.9205 | |
| ckim-vqsr | INDEL | * | * | hetalt | 95.4941 | 91.6313 | 99.6969 | 55.9167 | 23125 | 2112 | 23354 | 71 | 70 | 98.5915 | |
| ckim-vqsr | INDEL | * | * | homalt | 99.5675 | 99.8658 | 99.2711 | 58.9429 | 125004 | 168 | 125017 | 918 | 901 | 98.1481 | |
| ckim-vqsr | INDEL | * | HG002complexvar | * | 99.2578 | 98.8640 | 99.6548 | 58.2159 | 76064 | 874 | 75924 | 263 | 222 | 84.4106 | |
| ckim-vqsr | INDEL | * | HG002complexvar | het | 99.5556 | 99.3270 | 99.7852 | 57.9433 | 45901 | 311 | 45518 | 98 | 61 | 62.2449 | |
| ckim-vqsr | INDEL | * | HG002complexvar | hetalt | 91.5318 | 85.7259 | 98.1813 | 66.4504 | 3171 | 528 | 3401 | 63 | 63 | 100.0000 | |
| ckim-vqsr | INDEL | * | HG002complexvar | homalt | 99.7470 | 99.8705 | 99.6237 | 57.3434 | 26992 | 35 | 27005 | 102 | 98 | 96.0784 | |
| ckim-vqsr | INDEL | * | HG002compoundhet | * | 93.9622 | 92.7503 | 95.2061 | 62.6940 | 27788 | 2172 | 27665 | 1393 | 1381 | 99.1385 | |
| ckim-vqsr | INDEL | * | HG002compoundhet | het | 93.3882 | 98.2169 | 89.0120 | 79.6916 | 4021 | 73 | 3775 | 466 | 457 | 98.0687 | |
| ckim-vqsr | INDEL | * | HG002compoundhet | hetalt | 95.5428 | 91.6720 | 99.7550 | 50.3140 | 23083 | 2097 | 23206 | 57 | 57 | 100.0000 | |
| ckim-vqsr | INDEL | * | HG002compoundhet | homalt | 61.0714 | 99.7085 | 44.0154 | 84.7468 | 684 | 2 | 684 | 870 | 867 | 99.6552 | |
| ckim-vqsr | INDEL | * | decoy | * | 100.0000 | 100.0000 | 100.0000 | 99.9717 | 10 | 0 | 10 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | decoy | het | 100.0000 | 100.0000 | 100.0000 | 99.9801 | 6 | 0 | 6 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | decoy | hetalt | 100.0000 | 100.0000 | 100.0000 | 99.8485 | 1 | 0 | 1 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | decoy | homalt | 100.0000 | 100.0000 | 100.0000 | 99.9337 | 3 | 0 | 3 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | func_cds | * | 99.4421 | 99.7753 | 99.1111 | 54.2683 | 444 | 1 | 446 | 4 | 1 | 25.0000 | |
| ckim-vqsr | INDEL | * | func_cds | het | 99.3103 | 100.0000 | 98.6301 | 63.5607 | 214 | 0 | 216 | 3 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | func_cds | hetalt | 88.8889 | 80.0000 | 100.0000 | 50.0000 | 4 | 1 | 4 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | func_cds | homalt | 99.7792 | 100.0000 | 99.5595 | 39.4667 | 226 | 0 | 226 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.7235 | 93.8350 | 95.6289 | 69.0222 | 9452 | 621 | 9298 | 425 | 390 | 91.7647 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.3979 | 96.6584 | 94.1699 | 79.6348 | 3905 | 135 | 3602 | 223 | 191 | 85.6502 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.2704 | 87.7615 | 99.5173 | 36.9269 | 3356 | 468 | 3505 | 17 | 17 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5725 | 99.1852 | 92.2138 | 66.1587 | 2191 | 18 | 2191 | 185 | 182 | 98.3784 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_gt200bp_gt95identity_merged | * | 95.0000 | 95.0000 | 95.0000 | 99.3932 | 19 | 1 | 19 | 1 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_gt200bp_gt95identity_merged | het | 100.0000 | 100.0000 | 100.0000 | 99.4426 | 12 | 0 | 12 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_gt200bp_gt95identity_merged | hetalt | 100.0000 | 100.0000 | 100.0000 | 95.3846 | 3 | 0 | 3 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_gt200bp_gt95identity_merged | homalt | 80.0000 | 80.0000 | 80.0000 | 99.5362 | 4 | 1 | 4 | 1 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9460 | 98.5791 | 99.3156 | 73.7970 | 93107 | 1342 | 93014 | 641 | 576 | 89.8596 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3731 | 99.4054 | 99.3408 | 76.0979 | 47984 | 287 | 47771 | 317 | 259 | 81.7035 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.3917 | 93.3580 | 99.6293 | 58.1709 | 14393 | 1024 | 14513 | 54 | 54 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5126 | 99.8992 | 99.1290 | 74.4665 | 30730 | 31 | 30730 | 270 | 263 | 97.4074 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.0302 | 97.5303 | 98.5353 | 67.8515 | 63737 | 1614 | 63506 | 944 | 836 | 88.5593 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5995 | 98.7927 | 98.4071 | 74.5792 | 30112 | 368 | 29653 | 480 | 385 | 80.2083 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.1302 | 92.8764 | 99.6203 | 36.5800 | 15515 | 1190 | 15743 | 60 | 60 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.7459 | 99.6917 | 97.8179 | 67.5313 | 18110 | 56 | 18110 | 404 | 391 | 96.7822 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.6846 | 96.8924 | 98.4899 | 76.8920 | 2089 | 67 | 2087 | 32 | 20 | 62.5000 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.8744 | 97.2930 | 98.4628 | 79.3759 | 1222 | 34 | 1217 | 19 | 7 | 36.8421 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 90.4918 | 82.6347 | 100.0000 | 64.3038 | 138 | 29 | 141 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.8475 | 99.4543 | 98.2480 | 73.3285 | 729 | 4 | 729 | 13 | 13 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | * | 94.1176 | 94.1176 | 94.1176 | 99.4642 | 16 | 1 | 16 | 1 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | het | 100.0000 | 100.0000 | 100.0000 | 99.5157 | 10 | 0 | 10 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | hetalt | 100.0000 | 100.0000 | 100.0000 | 94.5455 | 3 | 0 | 3 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | homalt | 75.0000 | 75.0000 | 75.0000 | 99.6201 | 3 | 1 | 3 | 1 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.4518 | 99.2381 | 99.6663 | 75.2850 | 5080 | 39 | 5078 | 17 | 10 | 58.8235 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.5993 | 99.5000 | 99.6988 | 76.7994 | 2985 | 15 | 2979 | 9 | 4 | 44.4444 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 94.8354 | 90.5579 | 99.5370 | 73.1009 | 211 | 22 | 215 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7617 | 99.8940 | 99.6298 | 72.7247 | 1884 | 2 | 1884 | 7 | 5 | 71.4286 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.7375 | 99.6412 | 99.8341 | 75.9622 | 3610 | 13 | 3610 | 6 | 3 | 50.0000 | |