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while (<$IN2>) {
    chomp $_;
...
        }
    }
}

Use of uninitialized value in subtraction (-) at line 117, <$IN2> line
+ 4148567.
Use of uninitialized value in numeric gt (>) at line 118, <$IN2> line 
+4148567.
Use of uninitialized value $F2[2] in hash element at line 119, <$IN2> 
+line 4148567.
Argument "" isn't numeric in sort at line 127, <$IN2> line 4148567.

Line 117 - $store{(abs($F2[2]-$F3[2])+1)}++;
Line 118 - ($F2[2], $F3[2]) = ($F3[2], $F2[2]) if $F2[2] > $F3[2];
Line 119 - $Tally{$F2[1]}{$F2[2]}{$F3[2]}++;
Line 127 - foreach my $value1 (sort {$a <=> $b} keys %{$Tally{$chr}}) 
+{

w    11    99658    75    75M    0
c    11    99999    75    75M    74
...
c    10    177758    75    75M    74
w    10    177438    74    74M    0
w    7    185488    74    74M    0