PAV & Methylation
Differences Between Ecotypes

Interactive visualization of Presence-Absence Variation and DNA methylation differences between Lean and Siscowet lake trout ecotypes.

Lean (n=4) Siscowet (n=4)
Chromosome 1 NC_052307.1
Chromosome 2 NC_052308.1
Chromosome 3 NC_052309.1

Track Legend

Lean-Specific Variants

Insertions and deletions found exclusively in Lean trout samples (bc2041, bc2069, bc2070, bc2068).

Siscowet-Specific Variants

Insertions and deletions found exclusively in Siscowet trout samples (bc2071, bc2073, bc2072, bc2096).

Shared Variants

Structural variants present in both ecotypes, indicating ancestral polymorphisms.

Gene Annotations

Reference gene annotations from the SaNama_1.0 genome assembly (GCF_016432855.1).

About This Study

Ecotype Comparison

Lake trout exhibit remarkable morphological diversity. This study compares Lean and Siscowet ecotypes to understand genetic and epigenetic underpinnings of their phenotypic differences.

PacBio HiFi Sequencing

High-fidelity long-read sequencing enables detection of structural variants and native DNA methylation simultaneously, providing comprehensive genomic insights.

Open Science

All data, code, and analyses are publicly available on GitHub. This browser is deployed via GitHub Pages for easy access and reproducibility.

Sample Information

Sample ID Ecotype PAV Features Description
bc2041 Lean ~871K insertions, ~299K deletions Lean ecotype sample
bc2069 Lean ~341K insertions, ~217K deletions Lean ecotype sample
bc2070 Lean ~538K insertions, ~284K deletions Lean ecotype sample
bc2068 Lean ~332K insertions, ~262K deletions Lean ecotype sample
bc2071 Siscowet ~574K insertions, ~297K deletions Siscowet ecotype sample
bc2073 Siscowet ~652K insertions, ~308K deletions Siscowet ecotype sample
bc2072 Siscowet ~469K insertions, ~267K deletions Siscowet ecotype sample
bc2096 Siscowet ~1.04M insertions, ~347K deletions Siscowet ecotype sample