Fig. 1.

Phasing of the allelic relationships between noncoding regulatory regions and exonic regions. a, b An example of phasing by both physical (a) and synthetic (b) long-read technologies. The lines show an allelic relationship of multiple single- nucleotide variants (SNVs) of the SEMA6A gene in the H1975 cell line (previously reported in Sereewattanawoot et al. [21]). Each SNV is represented in a circle. c The scheme for identification of regulatory mutations affecting transcription and gene expression by phasing analysis [21]. Heterozygous regulatory mutations are associated with exonic variations in allele resolution using linked-read sequencing (left). The phasing results are validated by physical long reads. Allelic transcription and expression are also considered to evaluate the impact on regulatory mutations (right). The RNA-seq and ChIP-seq data are used to measure the transcription and expression statuses in allele level