map returns the value of the last expression evaluated within { #block }. The last expression you're evaluating is a substitution operator, and its value is a boolean value; true (1) if a match occurred, or false if there was no match. That's why it keeps passing '1' into @nar. If you want to return the result of the substitution, make sure that value is the last thing evaluated in { #block }.
@nar = map { # get rid of trailing number
my $st = ( split( " ", $_ ) )[0];
# replace bracket with S
$st =~ s/\[[ATCG]+\/S/g;
# return result value
$st;
} @arr;
...that ought to do it...
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