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==== What is QUAL? ====
==== What is QUAL? ====
QUAL stands for query quality. It is an indicator for how accurate each base in the query sequence (SEQ) is. If QUAL is specified, there is a quality value for each base in SEQ.
Quality is calculated based on the probability that a base is wrong, p, using the following formula:
<math>quality = -10 \log_{10}p</math>
This quality is called the [http://en.wikipedia.org/wiki/Phred_quality_score Phred Quality Score].
Since a human readable format is desired for SAM, 33 is added to the calculated quality in order to make it a printable character ranging from ! - ~.
So, for SAM, the QUAL field is:
<math>QUAL = (-10 \log_{10}p) + 33</math>
==== What are TAGs? ====
==== What are TAGs? ====
