Fig. 7: IGV plot of phased HG002 ONT reads and methylation calls by DeepMod2 in two imprinting control regions (ICRs) shown in GRCh38 coordinates. | Nature Communications

Fig. 7: IGV plot of phased HG002 ONT reads and methylation calls by DeepMod2 in two imprinting control regions (ICRs) shown in GRCh38 coordinates.

From: A signal processing and deep learning framework for methylation detection using Oxford Nanopore sequencing

Fig. 7: IGV plot of phased HG002 ONT reads and methylation calls by DeepMod2 in two imprinting control regions (ICRs) shown in GRCh38 coordinates.

The region on the left shows the ICR of H19/IGF2 gene cluster that is methylated only in the paternal allele, whereas the region on right shows the ICR of KCNQ1/KCNQ1OT1 gene cluster which is methylated only in the maternal allele. Reads in both regions belong to the same haplotype block with phasing done by NanoCaller. a Shows phased per-site output by DeepMod2, i.e. methylation frequency found in each haplotype. b Shows read coverage track with red and blue colors depicting the ratio of methylated and unmethylated reads, respectively, at each CpG site regardless of the phase. The methylation fraction calculated from all reads hovers in 0.4–0.6 range, but this fraction can be affected by uneven coverage between alleles. Phased methylation frequencies on the other hand Show a much more drastic difference between methylation frequencies of the alleles. c Shows phased ONT reads with methylation tags added by DeepMod2, with red and blue depicting methylated and unmethylated cytosines. d Shows RefSeq gene tracks for genes overlapping the two ICRs. Panels (a–d) are generated in IGV.

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