Re: [Samtools-help] What is the relation between alignment match an d sequence match/mismatch. .

[Rusch, M. <Mic...@ST...>]

Put another way, yes, both a sequence match and a sequence mismatch are an alignment match.

An alignment match simply means that when you align the read to the reference sequence, that read base lines up with a base in the reference.  A sequence match means that they line up and are the same letter.  A sequence mismatch means they line up and are different letters.

If it's not an alignment match, then it's an insertion or deletion (or skip), or it falls outside the range of the aligned region, such as soft- or hard-clipping.

Michael

-----Original Message-----
From: Peter Cock [mailto:p.j...@go...]
Sent: Friday, November 04, 2011 4:17 AM
To: Peng Yu
Cc: sam...@li...
Subject: Re: [Samtools-help] What is the relation between alignment match an d sequence match/mismatch. .

On Fri, Nov 4, 2011 at 2:56 AM, Peng Yu <pen...@gm...> wrote:
> Hi,
>
> I'm confused about alignment match and sequence match/mismatch. Does
> alignment match include both sequence match and mismatch. I don't see an
> example for the usage of = and X on page 1 of SAM spec. Could any expert
> give some examples to help me understand the differences?

e.g. A CIGAR string 3=1X6X can be written as 10M.

Most tools generate CIGAR strings using M only, the equals (match) and
X (mismatch) were added later.

Peter

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