AlignedSequence: The bases of the read sequence contained in this alignment record, without CIGAR operations applied (equivalent to SEQ in SAM). alignedSequence and alignedQuality may be shorter than the full read sequence and quality. This will occur if the alignment is part of a chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR for this read will begin/end with a hard clip operator that will indicate the length of the excised sequence.

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