Internal stop codons were found in a protein-coding gene

[xo2003]

Hi,

I executed BRAKER using the --fungus option for fungal genome prediction and identified a protein-coding gene (g7260) containing internal stop codons. Upon examining the results through IGV, I found no RNA evidence in the gene region. Below is the g7260 information extracted from braker.gtf. Additionally, g7260.t1 was not present in braker.aa and braker.codingseq. I am curious about the possible reasons for this observation. Any insights would be greatly appreciated.

Thank you!

scaffold3       GeneMark.hmm3   gene    8788684 8790492 .       -       .       g7260
scaffold3       GeneMark.hmm3   transcript      8788684 8790492 .       -       .       g7260.t1
scaffold3       GeneMark.hmm3   stop_codon      8788684 8788686 .       -       0       transcript_id "g7260.t1"; gene_id "g7260";
scaffold3       GeneMark.hmm3   mRNA    8788684 8790492 .       -       .       transcript_id "g7260.t1"; gene_id "g7260";
scaffold3       GeneMark.hmm3   CDS     8788684 8790492 .       -       0       transcript_id "g7260.t1"; gene_id "g7260";
scaffold3       GeneMark.hmm3   exon    8788684 8790492 .       -       0       transcript_id "g7260.t1"; gene_id "g7260";
scaffold3       GeneMark.hmm3   start_codon     8790490 8790492 .       -       0       transcript_id "g7260.t1"; gene_id "g7260";