[maker-devel] Question about phase for CDS with start codon

[Brian Hall]

Aloha,

I'm working with a gff produced by maker. (I didn't run the program 
myself, but I believe it was version 2.24.) Here are the lines in question:

scaffold00033    maker    CDS    729494    729949    .    -    2 
ID=107343;Name=BDOR_005037-RC:cds:250;Parent=107334
scaffold00033    maker    start_codon    729947    729949    . -    .    
ID=107349;Name=BDOR_005037-RB:start1;Parent=107334

If I understand correctly, the start codon in this reverse-strand CDS is 
from position 729949 to 729947 -- the first three bases in the CDS. 
However, the phase value for the CDS is 2, which essentially skips the 
start codon. Downstream software (tbl2asn) is kicking up a "missing 
start codon" error.

I have several hundred such issues in the gff for a single genome. They 
generally only occur on reverse-strand CDSs. Any ideas?

Sincerest apologies if this is a duplicate question or if I've provided 
incomplete information. I am new at this. Thanks for your help!

--Brian