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.

Nakken et al. BMC Genomics 2009 10:43   doi:10.1186/1471-2164-10-43