TABLE 2

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

Chimeric
LibraryR+: R1> <R2R−: <R2 R1>F+: R1> R2>F−: R2> R1>InterchromosomalToo largeToo small
ycnbwsp_20.980890.002180.000070.000070.000890.001510.00144
ycnbwsp_3-HE0.951220.001160.005380.005840.007320.002700.02639
ycnbwsp_7-HE0.978390.000550.002650.002530.001950.003550.01037
ycnbwsp_8-HE0.973940.000680.002500.002760.001580.005530.01300
  • 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).