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Old 06-09-2010, 09:19 AM   #2
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Location: Germany

Join Date: May 2010
Posts: 101

The base quality is also a place holder just as the * in the reads column.

I found similar occurrences in my data (created with samtools pileup -vcf), e.g.

chr14 65392038 T A 0 0 0 1 * W

Note that the weird consensus A must result from a floating underflow in the MAQ SNP calling model ( Although the FAQ answer says that this only happens in repetitive regions, the reference T is upper case and I just checked again in the UCSC Genome Browser for hg19 that there is no repeat. So I guess the reason is that there is only one read.
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