Raymond, you've probably figured this out already, but since I was looking
for discussion of these files, I'll answer your email. The SNP file doesn't
address gaps, doesn't depend on the contig mover. The three fields for
every genome represent the contig name (the fasta header line of the
sequence containing the position of the SNP), the position in that
particular contig (i.e. 1-based position of the SNP in that particular
fasta entry), and the position in the whole genome (i.e. if you
concatenated all contigs in order together into one sequence, what would be
the coordinate of the SNP). This last obviously applies to a "draft" or
multi-chromosomal genome that contains multiple fasta entries in one file;
if you're dealing with a single chromosome, then the "position in contig"
and "genome-wide position" will match.
~Joe
On Sat, Feb 28, 2015 at 4:16 AM, Raymond Wan <r...@cuhk.edu.hk> wrote:
>
> Dear Aaron (or anyone else who knows),
>
> I've noticed that the SNP file format has changed in version 2.4.0
> compared to
> what's mentioned here:
>
> http://darlinglab.org/mauve/user-guide/files.html
>
> The first column is still "SNP pattern". But what use to be coordinates
> for
> each genome has now tripled. For each genome there is now:
>
> sequence_1_Contig sequence_1_PosInContg sequence_1_GenWidePos1 ...
>
> Would I be correct in saying that:
>
> 1) *_Contig is null if it contributes a gap to the SNP pattern.
> Otherwise, it
> gives the range of the contig.
>
> 2) *_PosInContg is 0 if it contributes a gap to the SNP pattern;
> otherwise, it
> is the position within that contig.
>
> 3) *_GenWidePos1 is 0 if it contributes a gap to the SNP pattern;
> otherwise it
> is the position within that genome.
>
> I'm thinking aloud a bit. :-) But it sounds like the old SNP file is just
> column 3. Is that correct?
>
> However, I'm a bit puzzled what contig means in this context. Does it
> refer to
> usage of the Mauve Contig Mover? That is, if MCM isn't used, then columns
> (2)
> and columns (3) are identical in value? (This is what I'm noticing and I'm
> trying to understand why...I think this is the reason, since I haven't used
> MCM.)
>
> Thank you!
>
> Ray
>
>
>
>
> -------------------------------------------------
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>
>
>
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--
Joseph Fass
Bioinformatics Data Analyst
UC Davis Genome Center - Bioinformatics Core
http://bioinformatics.ucdavis.edu/
jnf...@ucdavis.edu
phone ~ 530.752.2698
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