How do you tell which coordinates are used in a .bam file? Well, its pretty easy. Just pull the .bam file header up using Samtools
Then check out the rows that begin with @SQ followed by SN:chr## and LN:########. Compare the lengths of a few of the chromosomes to the below list of lengths. Whichever list the lengths match will indicate which coordinates are being used in the .bam file.
Hope this is helpful in determining which coordinates are used in your .bam files.
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