As follow-up from our email discussion I wanted to see if you were able to successfully add the custom genome for Chimpanzee into GenomeBrowse?
You can curate your own reference sequence by converting the FASTA reference that was used to align your sequences and create your BAM files. To do this go to Add and select Convert in the lower left corner, add your FASTA file and follow the prompts to create the reference sequence.
You can find an example workflow for this process in a tutorial we have for our analytic software SVS at the following link, the process is very similar in GenomeBrowse.
Create Custom Genome Assembly
Once the conversion is complete you will want to close and reopen GenomeBrowse for the new source to be available, then select the new genome build from the assembly dropdown and your BAM files should correctly draw in GenomeBrowse.
Alternatively we can also create the reference sequence and have it available from our Public Annotations repository. If you can provide a link to a public source of the references sequence I can add it to our list of genomes to curate.
Let me know how I can help you further.