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SAM & BAM formats

SEQ field

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How paired-end reads are stored in SEQ field of SAM file? Choose correct statements.

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Both soft- and hard-clipping bases are shown

Sequence is represented in the 3' -> 5' direction

Sequence is represented in the 5' -> 3' direction

Sequence is aligned on the forward or reverse strand (but its mate read sequence aligns to the opposite one)

Hard-clipping bases are not shown

Sequence is aligned on the forward strand

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