mjhjmtu

A01 11814111 11814112 GA AA
A01 11485477 11485519 AG AT
A01 11667935 11667971 TC TA
A01 11876070 11876079 TC TG
A01 11613258 11613277 AC GC
A01 11876079 11876107 CA GA
A01 11616453 11616463 TA TG
A01 11875367 11875368 GG GA
A01 11667971 11667993 CA AA
A01 11564406 11564411 TA TG
A01 11477215 11477235 TG CG

The awk script to split the values of column 4 and 5 and then test these against each other pairwise. When a value differs between the two arrays, the string from the first column is printed with an underscore and the appropriate value from column 2 or 3. If both nucleotides are different, two lines of output are to be produced.
Also, print the differed values in col 4 and 5 against each id.

awk ' split($4, a1, ""); split($5, a2, ""); for (i in a1) if (a1[i] != a2[i]) print $1 "_" $(i+1) ' input > out

does the first part.

output needed as:

A01_11814111 G A

A01_11485519 G T

Contents of tmp.txt

A01 11814111 11814112 GA AA
A01 11485477 11485519 AG AT
A01 11667935 11667971 TC TA
A01 11876070 11876079 TC TG
A01 11613258 11613277 AC GC
A01 11876079 11876107 CA GA
A01 11616453 11616463 TA TG
A01 11875367 11875368 GG GA
A01 11667971 11667993 CA AA
A01 11564406 11564411 TA TG
A01 11477215 11477235 TG CG

Contents of tmp.awk

 if (substr($4,1,1) != substr($5,1,1)) 
 print $1 "_" $2 " " substr($4,1,1) " " substr($5,1,1);
 
 if (substr($4,2,1) != substr($5,2,1)) 
 print $1 "_" $3 " " substr($4,2,1) " " substr($5,2,1);
 

Sample output

[user@server ~]$ awk -f tmp.awk tmp.txt
A01_11814111 G A
A01_11485519 G T
A01_11667971 C A
A01_11876079 C G
A01_11613258 A G
A01_11876079 C G
A01_11616463 A G
A01_11875368 G A
A01_11667971 C A
A01_11564411 A G
A01_11477215 T C

Bonus. In bash

#!/bin/bash
while read line
do
 set $line
 if [ $4:0:1 != $5:0:1 ]
 then printf "$1_$2 $4:0:1 $5:0:1n"
 fi
 if [ $4:1:1 != $5:1:1 ]
 then printf "$1_$3 $4:1:1 $5:1:1n"
 fi
done < tmp.txt

Sample output

A01_11814111 G A
A01_11485519 G T
A01_11667971 C A
A01_11876079 C G
A01_11613258 A G
A01_11876079 C G
A01_11616463 A G
A01_11875368 G A
A01_11667971 C A
A01_11564411 A G
A01_11477215 T C

awk solution:

awk '
 split($4$5, arr, "");
 if(arr[1] == arr[3])
 print $1 "_" $3, arr[2], arr[4];
 else
 print $1 "_" $2, arr[1], arr[3];
' input.txt

sed solution:

sed -r ' 

 s@(w*) *(w*) *(w*) *(w)(w) *4(w)$@1_3 5 6@
 s@(w*) *(w*) *(w*) *(w)(w) *(w)5$@1_2 4 6@

' input.txt

Output (both the same)

A01_11814111 G A
A01_11485519 G T
A01_11667971 C A
A01_11876079 C G
A01_11613258 A G
A01_11876079 C G
A01_11616463 A G
A01_11875368 G A
A01_11667971 C A
A01_11564411 A G
A01_11477215 T C