Fig. 2

Variant calling in the KIV-2 VNTR of the LPA gene. A Targeted KIV-2 sequencing approaches selectively amplify all KIV-2 repeats by leveraging the high inter-repeats homology and exclude other kringles (I). All KIV-2 reads are aligned to a single KIV-2 reference repeat and KIV-2 mutations are called as low-level mutations (II). B In WES or WGS data, KIV-2 reads are mixed with reads originating from other kringles and homologous regions (I). When aligning the reads to a single KIV-2 reference repeat for variant calling as in previous approaches [2], reads that are nearly identical to KIV-2 can align and cause spurious variant calls (II)