IGV web app sequence track showing up on bam alignments and not on reference genome

[magn...@umn.edu]

Hello IGV-help,

I have loaded my genome and bam files using the igv-webapp-1.4.1 with Amazon s3. The sequence track is not showing up below my loaded genome, but sequence is showing up on my loaded .bam files. I cannot change the color of the tracks loaded because the sequence track is showing up on the reads even though these are not SNPs. How can I change this default? 

[Helga Thorvaldsdottir]

For others who may be reading this thread - the discussion was continued in the corresponding GitHub issue @ https://github.com/igvteam/igv/issues/1035