Fig. 4: Duplex detection of modified bases using High Duplex PromethION flow cells.

Reads from all replicates are concatenated here for visualisation. a Schematic summary of currently detectable modification states from duplex reads. b UpSet plot of CpG-context cytosine base-calls from all duplex reads. Produced using UpSetPlot (0.9.0)⁹⁴. Top: percentage of duplex reads described by the intersection matrix below. Below: percentage of duplex reads containing one or more of a given cytosine state. c IGV view of the Nespas-Gnasxl imprinted locus from nanopore duplex sequencing. Reads are separated by allele and have been down sampled for visualisation. Above: overview of the whole imprinted locus (chr2:174,134,000-174,145,000). Below: close-up IGV view of duplex modified base-calls over a 50 bp segment. Duplex modified bases appear as blocks of two consecutive modification calls, with the forward (top) modification indicated by the colour on the left and the reverse (bottom) modification indicated by the colour on the right. d Comparison of the mean percentage of all duplex modified base-calls in the whole genome, as in (b), to modified base-calls within the methylated and unmethylated alleles of 15 imprinted loci. Duplex base-calls across replicates are merged.