sam file field SEQ

In Samtools manual, the SEQ field is not fully defined.

SEQ: segment SEQuence. This field can be a ‘ * ’ when the sequence is not stored. If not a ‘*’, the lengthof the sequence must equal the sum of lengths ofM/I/S/=/Xoperations inCIGAR. An ‘=’ denotes thebase is identical to the reference base. No assumptions can be made on the letter cases.

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Bowtie2 will print read sequence in this field.

if aligned to the reverse strand, reverse-complemented reads sequence will be printed.

Tested, confirmed.

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BWA probably does it in the same way.

10 SEQ query SEQuence on the same strand as the reference

No test yet

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Samtools fasta/fastq
It dumps SEQ field but in Raw read style. Essentially, raw reads will be output.

For example:

A sequence with flag bit 16, means it is mapped to reverse strand. In SEQ field, a reverse complement sequence is stored in SEQ field. However, when outputing in samtools fasta, original sequence will be written out.