A   B    1/1:0,13:13:39:.:.:418,39,0          1/1:0,25:25:75:.:.:806,75,0

A   B    1/1:13,0:13:39:.:.:418,39,0          1/1:25,0:25:75:.:.:806,75,0

cat file | awk '{print $3}' | awk -F ":" '{print $2}'
0,13

awk ' BEGIN {FS=","; OFS=","}{print $2,$1}'
13,0