Fig. 2

Example of haplotype chains. Illustration of the inferred haplotype chains in a 250-bp region (position 57,415,050–57,415,300 on chromosome 20) in the GNAS locus from colon tumor B (see ‘Methods’). One major and two minor chains are inferred. The major chain is fully methylated while one of the minor chains is completely unmethylated. Each line is one read (green), with paired reads on the same line. Converted CpGs are marked in black. Bases not matching the reference genome are marked in red and are indicative of sequencing errors. The reads in the top part of a chain have an inferred forward direction, while the reads in the bottom part have an inferred reverse direction. After assigning reads to haplotypes chains, the epigenotype of a chain is inferred from all reads in the chain. The epigenotype is shown in the middle of each chain. An open circle is an unmethylated CpG site and a closed circle is an methylated CpG site. The chains continue beyond the right end point, but are cut for illustrative purposes