use Modern::Perl;

print "\n Enter the file name :>";
chomp( my $filename1 = <STDIN> );

open my $fh, '<', $filename1 or die "Cannot find the file $filename1: $!";
my @line = <$fh>;
close $fh;

open my $w, '>', 'Result.txt' or die "Cannot open the file Result.txt: $!";
print $w $line[0];

for (@line) {
    my ( $fourth, $tenth ) = ( split ' ' )[ 4, 10 ];
    print $w $_ if $fourth eq 'chr1' and $tenth eq 'chr1';
    # did you mean $fourth =~ /chr1/ and $tenth =~ /chr1/
}

close $w;