Metrics
Category Metrics
Overview
Metrics for evaluating the performance of whole genome sequencing experiments.This table summarizes the values that are specific to this metric.
| Metric | Summary |
|---|---|
| GENOME_TERRITORY | The number of non-N bases in the genome reference over which coverage will be evaluated. |
| MEAN_COVERAGE | The mean coverage in bases of the genome territory, after all filters are applied. |
| SD_COVERAGE | The standard deviation of coverage of the genome after all filters are applied. |
| MEDIAN_COVERAGE | The median coverage in bases of the genome territory, after all filters are applied. |
| MAD_COVERAGE | The median absolute deviation of coverage of the genome after all filters are applied. |
| PCT_EXC_ADAPTER | The fraction of aligned bases that were filtered out because they were in reads with mapping quality 0 and the looked like adapter reads. |
| PCT_EXC_MAPQ | The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (lower than MIN_MAPPING_QUALITY). |
| PCT_EXC_DUPE | The fraction of aligned bases that were filtered out because they were in reads marked as duplicates. |
| PCT_EXC_UNPAIRED | The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair. |
| PCT_EXC_BASEQ | The fraction of aligned bases that were filtered out because they were of low base quality (lower than MIN_BASE_QUALITY). |
| PCT_EXC_OVERLAP | The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads. |
| PCT_EXC_CAPPED | The fraction of aligned bases that were filtered out because they would have raised coverage above COVERAGE_CAP. |
| PCT_EXC_TOTAL | The total fraction of aligned bases excluded due to all filters. |
| PCT_1X | The fraction of bases that attained at least 1X sequence coverage in post-filtering bases. |
| PCT_5X | The fraction of bases that attained at least 5X sequence coverage in post-filtering bases. |
| PCT_10X | The fraction of bases that attained at least 10X sequence coverage in post-filtering bases. |
| PCT_15X | The fraction of bases that attained at least 15X sequence coverage in post-filtering bases. |
| PCT_20X | The fraction of bases that attained at least 20X sequence coverage in post-filtering bases. |
| PCT_25X | The fraction of bases that attained at least 25X sequence coverage in post-filtering bases. |
| PCT_30X | The fraction of bases that attained at least 30X sequence coverage in post-filtering bases. |
| PCT_40X | The fraction of bases that attained at least 40X sequence coverage in post-filtering bases. |
| PCT_50X | The fraction of bases that attained at least 50X sequence coverage in post-filtering bases. |
| PCT_60X | The fraction of bases that attained at least 60X sequence coverage in post-filtering bases. |
| PCT_70X | The fraction of bases that attained at least 70X sequence coverage in post-filtering bases. |
| PCT_80X | The fraction of bases that attained at least 80X sequence coverage in post-filtering bases. |
| PCT_90X | The fraction of bases that attained at least 90X sequence coverage in post-filtering bases. |
| PCT_100X | The fraction of bases that attained at least 100X sequence coverage in post-filtering bases. |
| FOLD_80_BASE_PENALTY | The fold over-coverage necessary to raise 80% of bases to the mean coverage level. |
| FOLD_90_BASE_PENALTY | The fold over-coverage necessary to raise 90% of bases to the mean coverage level. |
| FOLD_95_BASE_PENALTY | The fold over-coverage necessary to raise 95% of bases to the mean coverage level. |
| HET_SNP_SENSITIVITY | The theoretical HET SNP sensitivity. |
| HET_SNP_Q | The Phred Scaled Q Score of the theoretical HET SNP sensitivity. |
GATK version 4.5.0.0 built at Tue, 9 Jan 2024 14:37:17 -0500.
0 comments
Please sign in to leave a comment.