-
Notifications
You must be signed in to change notification settings - Fork 1
gc bias metrics
jprofijt edited this page Feb 17, 2020
·
1 revision
detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
| Attribute | Description |
|---|---|
| ACCUMILATION_LEVEL | ? |
| READS_USED | This option is used to mark including or excluding duplicates. |
| GC | The G+C content of the reference sequence represented by this bin |
| WINDOWS | The number of windows on the reference genome that have this G+C content |
| READ_STARTS | The number of reads whose start position is at the start of a window of this GC |
| MEAN_BASE_QUALITY | The mean quality of all bases of all reads that are assigned to windows of this GC |
| NORMALIZED_COVERAGE | the ration of "coverage" in this GC bin vs. the mean coverage of all GC bins. 1 represents mean coverage, < 1 is lower than mean coverage, > 1 means more coverage than the mean |
| SAMPLE | The sample to which these metrics apply. If null, it means they apply to all reads in the file. |
| LIBRARY | The library to which these metrics apply. If null, it means that the metrics were accumulated at the sample level. |
| READ_GROUP | The read group to which these metrics apply. If null, it means that the metrics were accumulated at the library or sample level. |