Fig. 1

Overview of KIV-2 LPA performance: A Genome wide alignment of short Illumina reads and long PacBio HiFi and ONT reads to LPA gene. We observed many non-unique mappings (i.e. mapping quality MQ = 0, shown in white) in KIV-2. The GRCh38 representation of KIV-2 contains six copies of the 5.5 kbp repeat, challenging even for longer reads. This is shown by many white (MQ = 0) PacBio reads and to a lesser extent for Oxford Nanopore Technologies (ONT) reads. The fraction of non-unique mapped reads increased with shorter reads, which often hindered the direct assessment of KIV-2 repeat copy number. B Total KIV-2 copy number compared between calls made by the DRAGEN LPA caller or using optical mapping technology, for cases where optical mapping spanned both genomic alleles. Dashed lines indicate error margins of 5% from optical mapping copy number. C Allelic KIV-2 copy number compared where the per-allele copy number was available from the DRAGEN LPA caller and from optical mapping assemblies. Dashed lines indicate error margins of 5% from optical mapping copy number