file1.db:
zm811463	1190	31050	-	A/G/T/C
zm811462	1190	31051	-	C/T
zm1829427	1190	31789	+	A/G
zm445312	1190	31883	-	A/G
zm5377419	1190	32419	+	A/C
zm1052506	1190	32829	+	C/G
zm1052507	1190	32886	+	A/C/T
zm9115338	1190	33832	+	A/G/CC

file2.query
1190	31277	A > T	1	0	0
1190	31607	C > A	0	3	1
1190	31629	C > T	0	2	0
1190	31789	A > G	1	2	5
1190	31882	A > C	0	4	0
1190	31883	T > A	0	4	0
1190	31883	T > C	2	2	5
1190	32199	C > T	0	1	1
1190	32487	T > C	0	1	1
1190	32496	A > G	0	3	0

output which i am getting now:
1190	31277	A > T	1	0	0	-
1190	31607	C > A	0	3	1	-
1190	31629	C > T	0	2	0	-
1190	31789	A > G	1	2	5	zm1829427
1190	31882	A > C	0	4	0	-
1190	32199	C > T	0	1	1	-
1190	32487	T > C	0	1	1	-
1190	32496	A > G	0	3	0	-

Total number of HITS: 1

BUT, i want my output look like:

1190	31277	A > T	1	0	0	-
1190	31607	C > A	0	3	1	-
1190	31629	C > T	0	2	0	-
1190	31789	A > G	1	2	5	zm1829427
1190	31882	A > C	0	4	0	-
1190	31883	T > A	0	4	0	-
1190	31883	T > C	2	2	5	-
1190	32199	C > T	0	1	1	-
1190	32487	T > C	0	1	1	-
1190	32496	A > G	0	3	0	-

Total number of HITS: 1

##</code><code>##

1190	31883	T > A	0	4	0       -
1190	31883	T > C	2	2	5       -

##</code><code>##

use strict;
use warnings;
use DB_File;


my $myhashfile = "hash.$$";
tie my %hash1, "DB_File", $myhashfile, O_RDWR|O_CREAT, 0666, $DB_HASH
    or die "cannot open file $myhashfile: $!";


open(OUT,">output.out")or die "can not open";
open(my $fh1, "<", "file1.db") or die "file1.db: $!";


foreach (<$fh1>){
    chomp;
    my @dbinfo = split(/\s+/);
    $hash1{"$dbinfo[1]#$dbinfo[2]"} = "$dbinfo[4]##$dbinfo[0]";
}
close($fh1);


my $c=0;
open(my $fh2, "<", "file2.query") or die "file2.query: $!";
my @snplist;
foreach (<$fh2>) {
chomp($_);@snplist=();

    my @queryinfo = split(/[\s>]+/);
    my $values = $hash1{"$queryinfo[0]#$queryinfo[1]"};
    my ($variant,$rs)=split("##",$values);

    my $flag_left=0;my $flag_right=0;
    @snplist=split("/",$variant);

    if(defined($variant)){ 
	foreach my $lis(@snplist){
		if($queryinfo[2] eq $lis){$flag_left=1;}
		elsif($queryinfo[3] eq $lis){$flag_right=1;}
	}

        if(($flag_left == 1) && ($flag_right == 1)){
		print OUT "$_\t$rs\n";
		$c++;
		$flag_left=0;$flag_right=0;
    	}
  }

  else{
	print OUT "$_\t-\n";
  }
}


print OUT "\nTotal number of HITS: $c\n";
close($fh2);

untie %hash1;
unlink($myhashfile);
$myhashfile=();