Fig. 7.

Haplotype chains near a CTCF site. The inferred haplotype chains in a small 500-bp region near the CTCF site at position 31,109,691 on chromosome 20 (same as in Fig. 6) in the LNCaP sample. Seven chains are found (black lines with open and closed circles). The two major chains are also shown in Fig. 6. The reads (green lines) assigned to a haplotype chain are shown above (inferred forward direction) and below (inferred reverse direction) the chain, with paired reads on the same line. Converted isolated CpGs are marked in blue and converted isolated GpCs in black. Bases not matching the reference genome are marked in red and indicative of errors (sequencing or bisulfite conversion). After assigning reads to haplotypes chains, the epigenotype of the chain is inferred from the reads: converted GpCs (solid black circles), unconverted GpCs (open black), and converted CpGs (open blue; there are only two of these)