Table 1.

Proportion of total SNVs accounted for by each SNV class at various minimum allele frequency (AF) thresholds and corresponding sum of squares differences (SSD) in SNV mutation spectra between FFPE and fresh frozen TCGA data

	Minimum AF threshold				Proportion of variants in fresh frozen data
SNV	no filter	0.05	0.1	0.15
A > C/T > G	0.017	0.026	0.054	0.051	0.061
A > G/T > C	0.100	0.165	0.286	0.372	0.126
A > T/T > A	0.015	0.023	0.009	0.013	0.087
C > A/G > T	0.017	0.026	0.063	0.064	0.186
C > G/G > C	0.012	0.023	0.036	0.051	0.175
C > T/G > A	0.839	0.737	0.554	0.449	0.366
SSD	0.287	0.193	0.102	0.103	0.000