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Old 03-28-2016, 07:05 PM   #2
Richard Finney
Senior Member
Location: bethesda

Join Date: Feb 2009
Posts: 700

3rd read flag value 401 has not primary alignment bit.

2nd read has "SA" tag:
SA is : Other canonical alignments in a chimeric alignment, formatted as a semicolon-delimited list: ( rname , pos , strand , CIGAR , mapQ , NM [[...]+. Each element in the list represents a part of the chimeric alignment. Conventionally, at a supplementary line, the [...] element points to the primary line.

it's pointing to 3rd read via the location.

So, looks like your software suppors reads that have parts that maps to different locations.
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