Post-alignment data. An example of the data available for analysis of methylation following alignment of the sequenced reads to a reference genome. The data are taken from Lister et al and show the first ten thousand bases of the positive strand of two samples of Arabidopsis in wild type (Col-0) and met1 knockout mutant. The number of times a cytosine is observed to be methylated is shown by the height of the coloured bars, with the colour indicating the context of methylation. The abundance of reported methylation is heavily dependent on the read coverage (black curve) at each base, which exhibits high variability.