And to prove that what the join utility does (see solution above) is not trivial but also not very complicated, let's try to emulate what it does in a short perl program.

perl -we 'open $_, "<", shift or die for my($D, $Q); my $p = -1e9999; 
+my $s = -1e9999; my $x; while (my $q = <$Q>) { chomp($q); my $k = (sp
+lit " ", $q)[1]; $p <= $k or die "query not sorted"; $p = $k; while (
+$s < $p and defined(my $d = <$D>)) { (my($l), $x) = (split " ", $d)[2
+,0]; $s <= $l or die "db not sorted"; $s = $l; } my $z = $p == $s ? $
+x : "-"; print $q, "    ", $z, "\n"; }' file1.db file2.query
[download]

The output is this.

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    zm445312
1190    31883    T > C    2    2    5    zm445312
1190    32199    C > T    0    1    1    -
1190    32487    T > C    0    1    1    -
1190    32496    A > G    0    3    0    -
[download]

It is an exercise to the reader to add the "Number of HITS" message.