Fig. 2

Read coverage and heterozygous positions in the primary mapping: The initial coverage of short-reads (SR) and long-reads (LR) against a generic locus-specific reference. Heterozygous positions (HP) and indels are colour-coded. HPs are shown by two colours, where both should, ideally, cover half of the height at a position. In this example, most HPs are present at the same position in both short-reads and long-reads. Observations of HPs that differ between short- and long-reads are common and are usually caused by differing allele imbalances between the two sequencing experiments. The clustering into two haplotypes is based on these HPs