Mismatch, Clip, and N Ratio
Summary
In this section, we introduce mismatch ratio, clip ratio, and N ratio for S, C, and N reads respectively. It is worthy of note that most of the time. BWA-backtrack does not report the condition of clips in SAM file. Thus, there is no clip rate analysis for such mapping algorithm.
| Label | Description |
|---|---|
| P | Perfectly-matched reads |
| S | Reads with substitution errors |
| C | Reads that contain clips |
| O | Reads with other errors |
| M | Multi-mapped reads |
| F | Unmapped reads |
| N | Reads that contain N |
Mismatch Ratio
If according to SAM file, a read can be mapped to reference assembly but with substitution errors (type S), we then compute its mismatch ratio as follows,
Mismatch ratio = No. of mismatch / read length
Reads whose mismatch ratio exceeds a specified threshold (default 20%) will be determined poorly-mapped.
SQUAT will plot the distribution of mismatch ratio for S reads in the report as follow,
Clip Ratio
If according to SAM file, a read can be mapped to reference assembly with clips marked on either side of the read (type C), we then compute its clip ratio as follows,
Clip Ratio = total length of clips / read length
Reads whose clip ratio exceeds a specified threshold (default 30%) will be determined poor quality.
SQUAT will plot the distribution of clip ratio for C reads in the report as follow,
N Ratio
If a read contains at least one 'N', we can also compute its N ratio as follows,
N Ratio = No. of N / read length
Reads whose N ratio exceeds a specified threshold (default 10%) will be determined poor quality.
| Threshold | Default value |
|---|---|
| Overall PM% | 20% |
| S ratio | 20% |
| C ratio | 30% |
| O ratio | 10% |
| N ratio | 10% |