Figure 8

Use of the Integrated Genome Viewer (IGV) showing an example of data at one locus in one subject. A) IGV view of a 45 kb window on chromosome 5. Reads should map to distinct regions (due to MspI digestion), and there should be an equivalent balance of forward and reverse reads. Gray shading represents perfect alignment with the HG19 standard human reference genome. B) Close-up of the region from A) showing that forward reads have a high proportion of red ‘T’s and reverse reads have a high proportion of green ‘A’s; IGV shows colored bases in gray reads when an error is detected. In this case, the read is perfectly aligned to the standard reference genome, but, due to bisulfite conversion, most ‘C’s have converted to ‘T’s (forward strand), and this is outputted in the IGV window. Diversity at a locus is partially generated by different methylation levels at specific CpG sites and sequencing errors.