Table 3.

Overrepresentation of marker lagging-strand mutations within putative OP sites

Lagging-strand mutations	T → C	G → A	T → A	T → G	C → A	G → C	Total
hTK
Total	12	64	14	4	1	2	97
OP sites	5	18	2	0	0	0	25
Overrepresentation (fold)	10.4	7.0	3.6	0.0	0.0	0.0
Normalized for nucleotide composition (fold)	7.8	4.1	2.7	N/A	N/A	N/A
GFP
Total	12	38	16	2	7	5	80
OP sites	2	5	5	1	1	4	18
Overrepresentation (fold)	2.9	2.3	5.4	8.6	2.5	13.8
Normalized for nucleotide composition (fold)	2.7	1.3	5.1	8.1	4.3	8.1
hTK and GFP
Total	24	102	30	6	8	7	177
OP sites	7	23	7	1	1	4	43
Overrepresentation (fold)	5.4	4.2	4.3	3.1	2.3	10.6
Normalized for nucleotide composition (fold)	4.5	2.5	3.6	2.6	4.9	6.4

Overrepresentation is defined as the percent of a given marker lagging-strand mutation within OP sites relative to the percent of the total, considering the fraction of sequence represented by these sites; in the case of hTK OP sites represent 4% of the total coverage, and in the case of GFP OP sites represent 5.8%. These values for overrepresentation were normalized by dividing the overrepresentation values by a ‘nucleotide composition bias factor’, a fudge factor expressing the relative abundance of individual nucleotides within OP sites (Supplementary Table S3). Values we were unable to calculate due to gaps in our data are indicated as N/A.