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Old 03-28-2016, 08:57 PM   #4
Richard Finney
Senior Member
Location: bethesda

Join Date: Feb 2009
Posts: 700

What is your goal?

What program is reporting the warning?

Check the manual for your alignment software and check the notes on when it produces an "SA" tag.

Read one is one mate pair.
The next two represent the other read with two entries , that is it is a "chimeric" read [ I think ].

Ignoring it could be thing to do, depending on your goals.

If you are looking for chimeric reads or possible errors in the reference, then you have struck gold
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