Fig. 1

Alignment of ICC 640 (top) and PM233 (bottom) Illumina and Nanopore reads to pseudochromosome Ca5 of the ICC 4958 v3.0 desi reference genome assembly [36], and expected amplicons (brown bars) A1 through A4, as defined in (Additional file 2: Table S1). The location of the CaNSP2 gene is depicted as a red arrow in the reference track. Its 5′-3′ orientation is left to right. The deletional gap in PM233 is shaded in yellow. The PM233 Nanopore reads that aligned to the left of the deletional gap are not continuous with those that aligned to the right of the gap