If the coordinates are integral and fewer than a few tens of million then you could simply generate a hash which uses coordinates as keys and averages as values then its a simple matter of looking up the hash for each marker:

use strict;
use warnings;
use lib 'C:\Users\Peter\Tools\BuildManager';

my $data = <<DATA;
12345 12445 0.454
12346 12446 0.326
12347 12447 0.355
DATA
my $markers = <<MARKERS;
12435
13455
13532
16135
MARKERS

my %dataLU;

open my $dataIn, '<', \$data;
while (defined (my $line = <$dataIn>)) {
    chomp $line;
    
    my ($start, $end, $avg) = split ' ', $line;
    
    $dataLU{$_}{sum} += $avg for $start .. $end;
    ++$dataLU{$_}{count} for $start .. $end;
}
close $dataIn;

open my $markersIn, '<', \$markers;
while (defined (my $line = <$markersIn>)) {
    chomp $line;
    next if ! length $line;
    
    if (! exists $dataLU{$line}) {
        print "No value for $line\n";
        next;
    }

    printf "Marker $line: %f\n", $dataLU{$line}{sum} / $dataLU{$line}{
+count};
}
close $markersIn;
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Prints:

Marker 12435: 0.378333
No value for 13455
No value for 13532
No value for 16135
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