TABLE 2.

Distribution of mapped genomic positions and orientations in the reference sequence of the first (R1) and second (R2) reads

		Chimeric
Library	R+: R1> <R2	R−: <R2 R1>	F+: R1> R2>	F−: R2> R1>	Interchromosomal	Too large	Too small
ycnbwsp_2	0.98089	0.00218	0.00007	0.00007	0.00089	0.00151	0.00144
ycnbwsp_3-HE	0.95122	0.00116	0.00538	0.00584	0.00732	0.00270	0.02639
ycnbwsp_7-HE	0.97839	0.00055	0.00265	0.00253	0.00195	0.00355	0.01037
ycnbwsp_8-HE	0.97394	0.00068	0.00250	0.00276	0.00158	0.00553	0.01300

These reads are from the clones of libraries constructed from whole-genome-amplified and unamplified DNA (see text). The proportions are based on the numbers reported by the Illumina CASAVA software (Summary.xml and anomaly.txt files). The second column, R+, is the proportion of normal (nonchimeric) clones in which the two reads from opposite ends of the clone are on alternative strands and the expected distance apart. In the R− column are clones in which the two reads map in divergent orientation. The F+ and F− columns list the proportions of clones in which the two reads map on the same strand and typically map within 10 kbp. These inverted chimeric clones (F+ and F−) are thought to arise via self-priming and have been reported to be more abundant in libraries derived from WGA DNA (Lasken and Stockwell 2007).