Reads (122 nucleotides) are sequenced from both ends of the amplicons (approximately 200 bp long). Therefore, some positions are sequenced from both reads (R and F for reverse and forward), which sometimes have inconsistent calls. At these positions we reject the F read call (respectively R read call) if 1) Cov(F) < 0.1 Cov(R) (respectively Cov(R) < 0.1 Cov(F)), where Cov indicates coverage depth at the examined position, or if 2) Pos(R) > Pos(F) (respectively Pos(F) > Pos(R)), where Pos indicates the distance in nucleotides from the read start.
