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On the gbrowse_details page for an alignment, the id of the target is used in the fasta line, implying (well, actually stating) that the sequence is of the query, whereas that sequence is always of the reference. I think this happens with all alignments, but here is an example using BAM data:
On the gbrowse_details page for an alignment, the id of the target is used in the fasta line, implying (well, actually stating) that the sequence is of the query, whereas that sequence is always of the reference. I think this happens with all alignments, but here is an example using BAM data:
http://www.rosaceae.org/gb/gbrowse_details/prunus_persica?ref=scaffold_2;start=4858736;end=4858808;name=HWI-EAS121%3A5%3A37%3A1256%3A1338%230;class=match;feature_id=HWI-EAS121%3A5%3A37%3A1256%3A1338%230%3B1%3B4858736%3B4858808%3B1;db_id=okinawa%3Adatabase
(note the T in the 6th position is from the reference.)
In addition to fixing this, it might be nice to add the query sequence fasta to the gbrowse_details page when it's available.
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