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Is it possible that on the same pileupcolumn object (i.e a specific aligned base) I find the same base but aligned to different strands? For example, can I find a coverage of 50 'A's that align to strand '+', and on the same time 50 'A's that align to strand '-' within the same index? I expect that if 'A' is aligned to strand '+', I will find 'T' aligned to strand '-'.

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    $\begingroup$ Please edit your question and clarify what you are doing. What code are you running? On what input? Anything is possible, including mismatched bases either in the real data or because of a sequencing error, but we can't know if you don't give us more details. $\endgroup$ – terdon Mar 26 at 14:55
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As @terdon mentions, it's certainly possible to have an A aligned on both strands. If a read has a mismatch at the location of interest and that mismatch is the complement of the reference base, then you are likely to see A in both strands. However, it is very unlikely you will see the same base at high coverage in both strands. For example, if your total coverage is 55, and you see 50 As on the + strand and 50 As on the - strand, it's likely that the pileup object is reporting the reverse complement sequence of the reads that align to the - strand for your convenience.

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