On Mon, Apr 23, 2012 at 5:56 PM, Sarah Hicks <garlicsc...@gmail.com> wrote:
> I am having trouble finding information on the MegaBLAST output
> columns. What is each column for? I can't seem to figure this out by
> comparing info in the columns to NCBI directly because the GI#'s don't
> match with the correct entry on NCBI. I've seen that others have
> posted about that problem, so I'm also waiting on details on that
> question, but for now, I'd just like to know what to make of the
> output...
> best,
> Sarah

I've not tried to track down this reported possible bug in GI numbers,
and weather it also affects BLAST+ as well as the legacy NCBI BLAST
(which has now been discontinued). Do you have a specific example.

As to the 12 columns, they are standard BLAST tabular output, and
should match the defaults in BLAST+ tabular output which are:

Column  NCBI name       Description
1       qseqid  Query Seq-id (ID of your sequence)
2       sseqid  Subject Seq-id (ID of the database hit)
3       pident  Percentage of identical matches
4       length  Alignment length
5       mismatch        Number of mismatches
6       gapopen         Number of gap openings
7       qstart  Start of alignment in query
8       qend    End of alignment in query
9       sstart  Start of alignment in subject (database hit)
10      send    End of alignment in subject (database hit)
11      evalue  Expectation value (E-value)
12      bitscore        Bit score

Peter
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