Hi

I am trying to understand SNP calling in Illumina pair-end sequencing. I am having 30 genotypes od a species. After mapping individually all genotypes to reference with BWA and processing through samtools, After that we a bam file for each genotype.

Now I am not understanding mpileup step to call SNP for each genotype.

For given gene we can I have two alleles, so they may have some nucleotide difference within genotypes than How we can call them as SNP when comparing with reference. see position 7

           1 2 3 4 5 6 7 8 9

Refere:    A T A T A T G C G

for    1 : A T A T A T A C G

for    2 : A T A T A T A C G

for    3 : A T A T A T A C G

rev    4 : A T A T A T G C G

for pair-end sequencing for can be forward read and rev can be reverse read from opposite strand. I am confused.