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Old 01-08-2011, 06:17 PM   #2
frozenlyse
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Location: Australia

Join Date: Sep 2008
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The flag of the first read (field 2) is 16 (0x10) which means that the read mapped to the reverse strand - the SAM format specifies that all alignments are to be represented on the forward strand, so the read is reported as the reverse complement, so the mismatches you are seeing are actually at the 3' end of the read
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