Structural variation between E. necator isolates estimated by sequencing depth analysis and qPCR. Line plot showing examples of genomic loci (A) without copy number variation (CNV), and (B) with CNV across the five genomes. Loci with copy number polymorphisms were detected by analyzing sequence read depth with CNV-seq . Gray boxes depict protein-coding sequences. (C) Validation by qPCR of CNV-seq copy number calls for four sample CNV loci in the five sequenced isolates. Scatterplots show the correlation between estimated copy numbers for both methods. A linear trend line is shown. Copy numbers by qPCR were estimated based on 2−ΔCt values normalized to the single copy E. necator elongation factor gene EnEF1 (En-g1817).