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<title>Per Base Sequence Quality</title>
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<style type="text/css">
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font-family: sans-serif;
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<h1>Per Base Sequence Quality</h1>
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This view shows an overview of the range of quality values across all bases
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at each position in the FastQ file.
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<p><img src="per_base_quality.png"></p>
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For each position a BoxWhisker type plot is drawn. The elements of the
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<li>The central red line is the median value</li>
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<li>The yellow box represents the inter-quartile range (25-75%)</li>
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<li>The upper and lower whiskers represent the 10% and 90% points</li>
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<li>The blue line represents the mean quality</li>
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The y-axis on the graph shows the quality scores. The higher the score
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the better the base call. The background of the graph divides the
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y axis into very good quality calls (green), calls of reasonable quality
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(orange), and calls of poor quality (red). The quality of calls on most
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platforms will degrade as the run progresses, so it is common to see
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base calls falling into the orange area towards the end of a read.
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It should be mentioned that there are number of different ways to encode
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a quality score in a FastQ file. FastQC attempts to automatically determine
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which encoding method was used, but in some very limited datasets it is
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possible that it will guess this incorrectly (ironically only when your
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data is universally very good!). The title of the graph will describe the
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encoding FastQC thinks your file used.
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A warning will be issued if the lower quartile for any base is less
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than 10, or if the median for any base is less than 25.
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This module will raise a failure if the lower quartile for any base is
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less than 5 or if the median for any base is less than 20.