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Old 06-11-2010, 06:34 PM   #3
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Location: The University of Melbourne, AUSTRALIA

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Originally Posted by luxmare View Post
I know that asterisks '*' in read bases column represent deletions as place holders in pileup format. But in my data, deletion '*' seems to has base quality score. why deleted bases have base qualities?
I don't know how samtools handles this particularly, but the IDEA of giving a deletion a "quality score" is good. A quality score is essentially just a logarithm of a "probability of error" or "probability that this is wrong". So you can interpret it as a statistical confidence of the deletion being real.
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