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Hi Stephen,

I was able to put together the reference allele track and assembly file for the E. coli genome. I will email them both to you for testing. For GenomeBrowse to correctly identify a reference for a BAM file the assembly file needs to contain the correct "chromosome" names and lengths for the genome, for the E. coli bacteria I was unable to find a consistent listing for the name so in the assembly file I have listed all the possible ones I could find.

Let me know if you have any issues and we can do some editing to get it to work.

Thanks, Jami...