Troubleshooting Common Problems
"Sequence x is lacking a reference" How do I create a
reference?
This error message occurs if you are submitting an alignment to
GenBank and one (or more) of the sequences in your alignment is
not linked to an original sequence document. This will occur if
you have imported the alignment into Geneious, but may also occur
if you have edited a sequence in the alignment and not applied the
changes to the original sequence (this will break the link to the
original sequence - see below).
Sequences in the alignment that are linked to an original
sequence document will have 
to
the left of the sequence name in the alignment. Clicking this link
will take you to the linked original sequence document. For
sequences in the alignment that are missing a linked original
sequence document, it is possible to create a reference sequence
without realigning the sequences. To do this, select the sequence
name in the alignment (this will select the entire sequence) and
click the Extract button. This will create a new sequence
document. If you are adding information to this sequence, for
example, collection data, add this information to the linked
reference sequence, ie the new sequence document in this case.
Geneious didn't ask if I wanted to apply the changes to my
original sequence
You may not see this question anymore if you have previously
answered the question and ticked the "Remember My Preference"
option. To reset the questions in Geneious, go to Tools→Preferences.
In the Appearance and Behavior tab click the Reset
questions button.
SeqID lcl:xxxxx is present on multiple Bioseqs in record
If two or more of the sequences you are submitting have the same Sequence ID you will get this error. The Sequence ID must contain a different value for each sequence in your submission, so that each sequence can be identified during the submission process before a unique accession number is assigned. You will need to check that you have chosen an appropriate document field for the Sequence ID in the Genbank Submission setup window.
Inconsistent taxnames
This error can occur when the organism name specified in the
Submit to Genebank window does not match the organism label in the
source annotation on your sequence. This often occurs if you have
inadvertently transferred a "Source" annotation from another
sequence to your sequence. This source annotation may not be
visible if the check box next to this annotation type is not
ticked in the Annotations panel. To fix this error, you will
either need to delete the source annotation or correct the
organism label on the source annotation so that it matches your
organism name exactly.
Illegal start codon used
NCBI will automatically generate the amino acid translation for
any CDS annotation using the transl_table and codon_start labels
on the annotation. This error message occurs when this translation
does not start with the start codon, M, and you have not specified
that the CDS is partial. To correct this, you will need to change
the transl_table and/or codon_start label using the Edit
Annotations window so that the first codon is a start codon.
Alternatively, if this CDS is a partial CDS sequence, open the Edit
Annotations window and double click on the annotation
interval. In the window that pops up, specify that the 5' end of
the annotation is truncated.
Missing stop codon
This error message occurs when the automatic translation of a CDS
annotation does not end with a stop codon and the CDS is not
labelled as partial. Check that the frame and translation table
for this annotation are correct, and, if not, change these
properties. Alternatively, if this CDS is a partial CDS sequence,
open the Edit Annotations window and double click on the
annotation interval. In the window that pops up, specify that the
3' end of the annotation is truncated.
Some mitochondrial genomes contain CDS's that do not include a
DNA-encoded stop codon. A stop codon is created after transcription
by polyadenylation, where the terminal 'T' or 'TA' of the transcript
is combined with the poly-A tail to form a 'TAA' stop codon. These
non-standard CDS's require an extra property attached to the CDS to
be acceptable for submission. You need to add the property transl_except
to the CDS. The figure below shows the format for this
property, pos:XXXX indicates the position of the terminal 'T'
nucleotide of the CDS, aa:term indicates that two A's should be
appended to the 3' terminus. If the CDS ends TA, then the
Value: would be (pos:1..2, aa:term) where 1 is
the sequence position of the 'T' nucleotide and 2 is the
position of the 'A'.
Missing qualifiers or features
Annotation qualifiers should be written in lowercase letters,
otherwise they will not be recognised. For example, if you write
the "product" qualifier, which is required for CDS and other amino
acid feature (e.g. tRNA) annotations, with a capital "P" (Product)
you will get error messages such as:
Missing encoded amino acid qualifier in tRNA feature, or
No protein BioSeq given FEATURE:CDS and
Expected CDS Product absent