position patient<-not in file, but for your reference!
34562	1048	t	t
30873	1048	t	t
25912	1048	N	N
25779	1048	t	t
26827	1048	t	t
24607	1048	t	t
22301	1048	t	t
24835	1048	t	t
24955	1048	N	N
25916	1048	N	N
22131	1048	t	t
22203	1048	t	t
23759	1048	t	t
23749	1048	t	t
18504	1048	t	t
20839	1048	c	t
34562	1082	c	c
30873	1082	c	c
25912	1082	N	N
25779	1082	c	c
26827	1082	c	c
24607	1082	c	c
22301	1082	c	c
24835	1082	c	c
24955	1082	N	N
25916	1082	N	N
22131	1082	c	c
22203	1082	c	c
23759	1082	c	c
23749	1082	c	c
18504	1082	c	c
20839	1082	c	c

##</code><code>##

#! C:\Perl\bin\perl 

use warnings;
use strict;

chomp(my $input=<STDIN>);
open (INPUT, "$input") or die "Cannot open file: $!";

chomp(my $number_positions=<STDIN>);

chomp(my $patient_number=<STDIN>);

chomp(my $output=<STDIN>);
open (OUTPUT, ">$output.txt") or die "Cannot open file: $!";

my @prettybase=<INPUT>;
close (INPUT);
my (@a,@c,@t,@g,@n,@a2,@c2,@t2,@g2,@n2);
my ($position, $letter1, $letter2, $patient);

for (my $k=0;$k<$number_positions; $k++) {
   @a=@c=@t=@g=@n=@a2=@c2=@t2=@g2=@n2=();
   $position="0";
   for (my $i=0;$i<=$patient_number; $i++) {
      ($position, $patient, $letter1, $letter2)=split(/\t/, $prettybase[$i]);
      if ($letter1=~ /[aA]/) {push ( @a, $letter1);}
      if ($letter1=~ /[cC]/) {push ( @c, $letter1);}
      if ($letter1=~ /[tT]/) {push ( @t, $letter1);}
      if ($letter1=~ /[gG]/) {push ( @g, $letter1);}
      if ($letter1=~ /[nN]/) {push ( @n, $letter1);}
      if ($letter2=~ /[aA]/) {push ( @a2, $letter2);}
      if ($letter2=~ /[cC]/) {push ( @c2, $letter2);}
      if ($letter2=~ /[tT]/) {push ( @t2, $letter2);}
      if ($letter2=~ /[gG]/) {push ( @g2, $letter2);}
      if ($letter2=~ /[nN]/) {push ( @n2, $letter2);}
      }
   my $number_a=scalar @a;
   #print "$number_a";
   my $number_c=scalar @c;
   #print "$number_c";
   my $number_t=scalar @t;
   my $number_g=scalar @g;
   my $number_n=scalar @n;
   my $number_a2=scalar @a2;
   my $number_c2=scalar @c2;
   my $number_t2=scalar @t2;
   my $number_g2=scalar @g2;
   my $number_n2=scalar @n2;

   my $percent_a=((("$number_a")/("$number_a"+"$number_c"+"$number_t"+"$number_g"+"$number_n")) * 100);
   my $percent_c=((("$number_c")/("$number_a"+"$number_c"+"$number_t"+"$number_g"+"$number_n")) * 100);
   my $percent_t=((("$number_t")/("$number_a"+"$number_c"+"$number_t"+"$number_g"+"$number_n")) * 100);
   my $percent_g=((("$number_g")/("$number_a"+"$number_c"+"$number_t"+"$number_g"+"$number_n")) * 100);
   my $percent_n=((("$number_n")/("$number_a"+"$number_c"+"$number_t"+"$number_g"+"$number_n")) * 100);
   my $percent_a2=((("$number_a2")/("$number_a2"+"$number_c2"+"$number_t2"+"$number_g2"+"$number_n2")) * 100);
   my $percent_c2=((("$number_c2")/("$number_a2"+"$number_c2"+"$number_t2"+"$number_g2"+"$number_n2")) * 100);
   my $percent_t2=((("$number_t2")/("$number_a2"+"$number_c2"+"$number_t2"+"$number_g2"+"$number_n2")) * 100);
   my $percent_g2=((("$number_g2")/("$number_a2"+"$number_c2"+"$number_t2"+"$number_g2"+"$number_n2")) * 100);
   my $percent_n2=((("$number_n2")/("$number_a2"+"$number_c2"+"$number_t2"+"$number_g2"+"$number_n2")) * 100);
   
   print OUTPUT "Position\#\: $patient\n";
   print OUTPUT "\tAllele 1  Allele 1 percentage\n";
   print OUTPUT "A:\t$number_a\t$percent_a\%\n\n";
   print OUTPUT "C:\t$number_c\t$percent_c\%\n\n";
   print OUTPUT "T:\t$number_t\t$percent_t\%\n\n";
   print OUTPUT "G:\t$number_g\t$percent_g\%\n\n";
   print OUTPUT "N:\t$number_n\t$percent_n\%\n\n";
   print OUTPUT "\tAllele 2  Allele 2 percentage\n";
   print OUTPUT "A:\t$number_a2\t$percent_a2\%\n\n";
   print OUTPUT "C:\t$number_c2\t$percent_c2\%\n\n";
   print OUTPUT "T:\t$number_t2\t$percent_t2\%\n\n";
   print OUTPUT "G:\t$number_g2\t$percent_g2\%\n\n";
   print OUTPUT "N:\t$number_n2\t$percent_n2\%\n\n";
}
close (INPUT);
close (OUTPUT);
_____ output_____
Position#: 1048
	Allele 1  Allele 1 percentage
A:	0	0%

C:	1	1.5625%

T:	56	87.5%

G:	0	0%

N:	7	10.9375%

	Allele 2  Allele 2 percentage
A:	0	0%

C:	0	0%

T:	57	89.0625%

G:	0	0%

N:	7	10.9375%
etc....