Table 2.

Substitution frequencies at sequence contexts associated with DNA sequencing errors

Substitution context	SNPs	DIMs
A(G/H)N	14.24 (158,901/1,115,692)	14.62 (50,277/343,864)
C(A/Y)C	0.38 (4,250/1,115,692)	0.45 (1,542/343,864)
G(A/C)C	1.14 (12,697/1,115,692)	1.42 (4,866/343,864)

A comparison of nucleotide substitution percentages in DIMs and high-quality SNPs at three sequence contexts previously shown to be overrepresented in false positive SNPs [27]. The percentages of substitutions are shown along with raw counts in parentheses. H stands for A, C or T, Y stands for C or T and N stands for any base.