Fig. 7

Final mapping of long-reads and short-reads to the refined, haplotype-specific references: Heterozygous positions (HP) and indels are colour-coded. Purple bars in the coverage plot (e.g. at position \(\sim 400\) bp in haplotype B) visualise deletions that are present in the short-read mappings of both haplotypes and indicate spurious insertions or positions that are hard to resolve using long-reads alone. Bicoloured positions denote existing ambiguities in the final mapping, in this example caused by positions where short-reads are not clustered with the two haplotypes as expected (e.g. at position 790 in haplotype A). It is still possible to resolve such positions using long-reads, even if they were not used for the initial haplotype clustering. The final consensus sequences are derived from these mappings