There are some classes of Augustus output genes that are a bit puzzling, such as the one below. The transcript starts with an intron and then the following (first) CDS fragment has a non-zero phase value, which goes against the GFF specification (in my understanding of it.) This needs to be checked and corrected for.
# start gene g856
NODE_4651_length_1024_cov_24.708984 AUGUSTUS gene 1 1068 0.91 + . g856
NODE_4651_length_1024_cov_24.708984 AUGUSTUS transcript 1 1068 0.91 + . g856.t1
NODE_4651_length_1024_cov_24.708984 AUGUSTUS intron 1 106 0.91 + . transcript_id "g856.t1"; gene_id "g856";
NODE_4651_length_1024_cov_24.708984 AUGUSTUS CDS 107 1068 0.91 + 2 transcript_id "g856.t1"; gene_id "g856";
NODE_4651_length_1024_cov_24.708984 AUGUSTUS stop_codon 1066 1068 . + 0 transcript_id "g856.t1"; gene_id "g856";
# protein sequence = [TQTSTAQSQAMDAESNTSTDPKNGDSQSALVQQLCQTVERLTNELSQARHEIQHLQERINTINSTTTPLSPLEFPTLQ
# ESQIRSTAFPDAPWNNPSKIQALKQPSIQRSEQRRMQREATAARFFQPPSENQGFKYLYIPTKARIPVGTIRTTFRKLGVNNARLLDIHYPARNTVAV
# LIHNDYEAEFVELLTRKNVHIRTDFTPFNGKILADPKYTSLPQEERDSIAIRLQKLRLSRALDYIRSPVKYAVARYFLDQEWISRTRYEEIMADRYNT
# KLTSIFDQTSQQQTTQDTFNDVSDNDLNMEAIDELPTGTSSPALH]
# Evidence for and against this transcript:
# % of transcript supported by hints (any source): 0
# CDS exons: 0/1
# CDS introns: 0/1
#5'UTR exons and introns: 0/0
#3'UTR exons and introns: 0/0
# hint groups fully obeyed: 0
# incompatible hint groups: 0
# end gene g856
There are some classes of Augustus output genes that are a bit puzzling, such as the one below. The transcript starts with an intron and then the following (first) CDS fragment has a non-zero phase value, which goes against the GFF specification (in my understanding of it.) This needs to be checked and corrected for.