Which read(s):
1. contain either a SNP (a single nucleotide polymorphism) or a position where different members of a multi-gene family have a different base?
C
2. doesn't have any DNA?
B
3. is a PCR product?
A, B, and C. All of three reads were obtained by sequencing PCR products, generated with the same set of primers.
The quality plots that I refer to are here.