A deletion and SNP in ALPK2 in U87MG. SRMA was applied to the alignments produced with BFAST of a human cancer cell line (U87MG; SRA009912.1). (a,b) The resulting alignments from within the coding region of ALPK2 (chr18:54,355,303-54,355,477) are shown before applying SRMA (a) and after applying SRMA (b). In this haploid region, Sanger sequencing confirmed a 15-bp deletion and a C-to-T SNP eight bases downstream of the deletion. Panel (a) shows the difficulty of aligning sequence reads from a region with a large deletion and a SNP, as false variation is observed (SNPs and indels). Nevertheless, some reads in (a) (BFAST) do correctly observe the deletion and SNP, which are therefore included in the variant graph created by SRMA. After local re-alignment using SRMA (b), the majority of the reads support the presence of the deletion and SNP, while false variation has been eliminated. The Integrated Genomics Viewer was used to view the alignments .