$ cat File1
13 18 1 + chromosome 1, 122638287 AGAGTATGGTCGCGGTTG
13 18 1 + chromosome 1, 128904080 AGAGTATGGTCGCGGTTG
13 18 1 - chromosome 14, 13627938 CAACCGCGACCATACTCT
13 18 1 + chromosome 1, 187172197 AGAGTATGGTCGCGGTTG
13 18 1 - chromosome X, 38407155 CAACCGCGACCATACTCT
13 18 1 + chromosome 9, 13503259 AGAGTATGGTCGCGGTTG
13 18 1 - chromosome 2, 105480832 CAACCGCGACCATACTCT
13 18 1 + chromosome 9, 49045535 AGAGTATGGTCGCGGTTG
13 18 1 + chromosome 1, 178729626 AGAGTATGGTCGCGGTTG
13 18 1 - chromosome X, 55081462 CAACCGCGACCATACTCT
9 17 2 + chromosome 10, 101398385 GCCAGTTCTACAGTCCG
9 17 2 - chromosome 3, 103818009 CGGACTGTAGAACTGGC
9 17 2 - chromosome 16, 94552245 CGGACTGTAGAACTGGC
4 18 1 - chromosome 18, 70056996 TACCCAACAACACATAGT
$ cat polsum.pl
use warnings;
use strict;

@ARGV == 1 or die qq[Usage: perl $0 input-file\n];

my ($number, @block_lines, $prev, @f);

while ( <> ) {
        next if /\A\s*\z/;
        chomp;
        @f = split;

        if ( $. == 1 ) {
                ++$number;
                push @block_lines, $_;
                next;
        }


        if ( $prev == $f[0] ) {
                ++$number;
        }
        else {
                if ( $number != 10 ) {
                        printf "%s\n", join qq[\n], @block_lines;
                }
                $number = 1;
                @block_lines = ();
        }

        push @block_lines, $_;
}
continue {
        $prev = $f[0];
        if ( eof() && $number != 10 ) {
                printf "%s\n", join qq[\n], @block_lines;
        }
}
$ perl polsum.pl File1 
9 17 2 + chromosome 10, 101398385 GCCAGTTCTACAGTCCG
9 17 2 - chromosome 3, 103818009 CGGACTGTAGAACTGGC
9 17 2 - chromosome 16, 94552245 CGGACTGTAGAACTGGC
4 18 1 - chromosome 18, 70056996 TACCCAACAACACATAGT

#! /usr/local/bin/perl
open(FILE,"<File1") or die("unable to open file");
my @mContent = <FILE>;
my %mFinal = ();
foreach ( @mContent )
{
   my $mLine = $_;
#   chomp ( $mLine );
   my $mField = (split(/ /,$mLine,999))[0];
   $mFinal{$mField}{"count"}=$mFinal{$mField}{"count"}+1;
   $mFinal{$mField}{"content"}.=$mLine;   # '.' for concatenate strings.
}
foreach my $mField ( keys %mFinal )
{
   my $mCount = $mFinal{$mField}{"count"};
   if ( $mCount != 10 )
   {
#      print "$mFinal{$mField}{'content'}\n";
      print "$mFinal{$mField}{'content'}";
   }
}