Evaluating absolute and chromosome-normalized metrics for ER visualization

To compare ERs across diverse taxa, we evaluated how absolute and chromosome-relative metrics influence the visualization and interpretation of ER diversity.

We considered two chromosome-relative measures: ΔGC, defined as the difference between the GC content of an ER and that of its chromosome (ΔGC = GC_ER − GC_chr), and %chr, defined as the size of the ER expressed as a percentage of its chromosome (100 × ER size / chromosome size).

GC content exhibits a strong and consistent host-linked signal across phyla, supporting the use of ΔGC as a biologically meaningful normalization. In contrast, %chr does not show a universal or stable relationship with chromosome size, but is included for methodological completeness.

We generated four comparative two-dimensional plots using all ERs:

1. Absolute GC (%) vs. absolute size (bp)
2. ΔGC vs. absolute size (bp)
3. Absolute GC (%) vs. %chr
4. ΔGC vs. %chr

Two complementary visualization modes are provided. In the first, chromosomes are plotted together with ERs. In the second, only ERs are shown, with axes scaled to ER ranges.

Interactive visualizations

• Chromosomes + ERs, linear scale
• Chromosomes + ERs, log10 scale
• ER-only, linear scale
• ER-only, log10 scale

Together, these visualizations allow direct assessment of how absolute versus chromosome-normalized metrics shape the apparent structure of ER diversity in feature space.