Hello,
Using a consesnsus sequence I am looking at individuals from a population in order to detect SNPS then create haplotypes. The SNP caller I am using is Freebayes. Freebayes is calling multiple SNPS and noticing that at that SNP all the invidivudals are heterozygous. The consensus sequence at that base is C and when I look at the mapping in IGV it is clear that half of the bases are A. All the A bases are of very low quality and fall at the end of read. The average ratio is roughly 25:75, A:C. This is seen in all individuals at this locus. The organism is diploid which would make this very strange. Is this just an artifact? Is this just an error or could this be a SNP?
The data is paired-end illumina data.
Thanks!