# Per Base Sequence Quality

## Summary

This view shows an overview of the range of quality values across all bases at each position in the FastQ file.

For each position a BoxWhisker type plot is drawn. The elements of the plot are as follows:

- The central red line is the median value
- The yellow box represents the inter-quartile range (25-75%)
- The upper and lower whiskers represent the 10% and 90% points
- The blue line represents the mean quality

The y-axis on the graph shows the quality scores. The higher the score the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

It should be mentioned that there are number of different ways to encode a quality score in a FastQ file. FastQC attempts to automatically determine which encoding method was used, but in some very limited datasets it is possible that it will guess this incorrectly (ironically only when your data is universally very good!). The title of the graph will describe the encoding FastQC thinks your file used.

## Warning

A warning will be issued if the lower quartile for any base is less than 10, or if the median for any base is less than 25.

## Failure

This module will raise a failure if the lower quartile for any base is less than 5 or if the median for any base is less than 20.