This gives your "expected output" but there's a conflict between my sort and your sort description. 

#!/usr/bin/perl -l

# http://perlmonks.org/?node_id=1198131

use strict;
use warnings;

my %one;

while(<DATA>)
  {
  my ($one, $two, $three, $four) = split;
  push @{ $one{$one} }, [ $two, $three, $four ];
  }

for my $one (sort keys %one)
  {
  my %groups;
LOOP:
  for ( sort {
    $a->[1] cmp $b->[1] or
    $b->[2] <=> $a->[2] or
    $a->[0] <=> $b->[0] }
    @{ $one{$one} } )
    {
    my ( $two, $three, $four ) = @$_;

    if( keys %groups )
      {
      for ( sort keys %groups )
        {
        if( ( $_ ^ "$three" ) =~ tr/\0//c <= 2 )
          {
          push @{ $groups{$_} }, [ $two, $three, $four ];
          next LOOP;
          }
        }
      push @{ $groups{$three} }, [ $two, $three, $four ];
      }
    else
      {
      push @{ $groups{$three} }, [ $two, $three, $four ];
      }
    }
  for ( sort keys %groups )
    {
    print 'CLUSTER';
    for ( values @{ $groups{$_} } )
      {
      print join "\t", $one, @$_;
      }
    }
  }

__DATA__
chrM:307    0    AGCGGGGA    129
chrM:307    0    AGCGGGGA    130
chrM:307    0    AGCGGGGA    129
chrM:308    0    AGCGGGGA    129
chrM:308    0    AGCGGGGA    130
chrM:308    0    AGCGGGGA    129
chrM:309    0    AGCGGGGA    129
chrM:309    0    AGCGGGGA    130
chrM:309    0    AGCGGGGA    129
chrM:307    0    TCAAAATG    130
chrM:308    0    TCAAAATG    130
chrM:309    0    TCAAAATG    130
chrM:307    0    TCACGGTG    130
chrM:308    0    TCACGGTG    130
chrM:309    0    TCACGGTG    130
chrM:307    0    TCAGCCTG    129
chrM:308    0    TCAGCCTG    129
chrM:309    0    TCAGCCTG    129
chrM:307    0    TCAGGGAG    130
chrM:308    0    TCAGGGAG    130
chrM:309    0    TCAGGGAG    130
chrM:307    1    TCAGGGTG    106
chrM:307    2    TCAGGGTG    130
chrM:307    2    TCAGGGTG    129
chrM:308    1    TCAGGGTG    106
chrM:308    2    TCAGGGTG    130
chrM:308    2    TCAGGGTG    129
chrM:309    1    TCAGGGTG    106
chrM:309    2    TCAGGGTG    130
chrM:309    2    TCAGGGTG    129

[download]

Output: 

CLUSTER
chrM:307        0       AGCGGGGA        130
chrM:307        0       AGCGGGGA        129
chrM:307        0       AGCGGGGA        129
CLUSTER
chrM:307        0       TCAAAATG        130
CLUSTER
chrM:307        0       TCACGGTG        130
chrM:307        0       TCAGGGAG        130
chrM:307        2       TCAGGGTG        130
chrM:307        2       TCAGGGTG        129
chrM:307        1       TCAGGGTG        106
CLUSTER
chrM:307        0       TCAGCCTG        129
CLUSTER
chrM:308        0       AGCGGGGA        130
chrM:308        0       AGCGGGGA        129
chrM:308        0       AGCGGGGA        129
CLUSTER
chrM:308        0       TCAAAATG        130
CLUSTER
chrM:308        0       TCACGGTG        130
chrM:308        0       TCAGGGAG        130
chrM:308        2       TCAGGGTG        130
chrM:308        2       TCAGGGTG        129
chrM:308        1       TCAGGGTG        106
CLUSTER
chrM:308        0       TCAGCCTG        129
CLUSTER
chrM:309        0       AGCGGGGA        130
chrM:309        0       AGCGGGGA        129
chrM:309        0       AGCGGGGA        129
CLUSTER
chrM:309        0       TCAAAATG        130
CLUSTER
chrM:309        0       TCACGGTG        130
chrM:309        0       TCAGGGAG        130
chrM:309        2       TCAGGGTG        130
chrM:309        2       TCAGGGTG        129
chrM:309        1       TCAGGGTG        106
CLUSTER
chrM:309        0       TCAGCCTG        129

[download]

In reply to Re: Find duplicate based on specific fields while allowing 2 mismatch by tybalt89
in thread Find duplicate based on specific fields while allowing 2 mismatch by amitgsir

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