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use strict;
use warnings;
...

print Dumper \%chrHash;

Count for chr1 3: 2
Locations for chr1 3: 100 300
...
                             ]
                    }
        };

$chrHash{$_} = { %countHash } for @chromosomes;

map { $chrHash{$_} = { %countHash } } @chromosomes;

use strict;
use warnings;
...
if ( first { $line[2] eq $_ } @chromosomes ) {
    print "Found $line[2] using first!\n";
}

Found chr5 using grep!
Found chr5 using first!