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SAM flag
Hello, I have a question regarding 0x0002 flag - the read is mapped in a proper pair. When read is mapped in a proper pair, does that mean that both pairs are aligned to the same contig?
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, does that mean that both pairs are aligned to the same contig?
well the formal definition of properly paired is:
each segment properly aligned according to the aligner
but yes, 99.999% it means than both reads of a pair are mapped on the same chromosome, with a different strand (FR), at a "good" distance from each other.
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