# Mapping

### Read-Level Metrics

| Metric            | Description                                                                     |
| ----------------- | ------------------------------------------------------------------------------- |
| Total input reads | Total number of input reads                                                     |
| QC-failed reads   | Total number of reads failing one or more quality checks                        |
| % QC-failed       | Percentage of reads failing one or more quality checks                          |
| Unique reads      | Total number of unique reads                                                    |
| % Unique          | Percentage of reads that are unique                                             |
| Mapped reads      | Total number of mapped reads, adjusted for filtered and excluded targets        |
| % Mapped          | Percentage of reads that are mapped, adjusted for filtered and excluded targets |

### Base-Level Metrics

| Metric      | Description                                          |
| ----------- | ---------------------------------------------------- |
| Total Bases | Total number of input bases                          |
| Mapped R1   | Total number of mapped bases on R1                   |
| % Mapped R1 | Percentage of R1 bases mapped                        |
| % Q30 R1    | Percentage of R1 bases with phred quality score >=30 |

### Deduplication

The deduplication bar chart reflects the ratio of unique and deduplicated reads.

### Read MAPQs

The read MAPQs bar chart reflects the percent of reads in various categories of phred quality score (Q0-Q10, Q10-Q20, Q20-Q30, Q30-Q40, Q40+).


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