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1    7    848773    75    A    74
1    7    848576    74    A    0
2    16    785802    75    A    0
2    16    786009    75    A    74
3    7    848576    75    A    74
3    7    848773    74    A    0

7    848576    848773    2
16  785802    786009    1

    my @F2 = split("\t", $_);
    my $partner = <$IN2>;
    my @F3 = split("\t", $partner);

my %count;
$count{$F2[1]}{$F2[2]}{$F3[2]}++;