Interactive visualization of Presence-Absence Variation and DNA methylation differences between Lean and Siscowet lake trout ecotypes.
Insertions (770,891) and deletions (225,337) found exclusively in Lean trout samples.
Insertions (1,086,799) and deletions (245,906) found exclusively in Siscowet trout samples.
3,465 deletions (>100bp) present in ALL 4 Siscowet samples and absent from ALL 4 Lean samples. High-confidence ecotype-specific variants.
Shared insertions (672,773) and deletions (205,599) present in both ecotypes.
Reference gene annotations from the SaNama_1.0 genome assembly (GCF_016432855.1).
302 total DMRs: 20 hypermethylated and 282 hypomethylated in Siscowet (p < 0.05, ≥15% diff).
Methylation difference (Siscowet - Lean) from 540,040 CpG sites with 4,440 significant DMCs.
Lake trout exhibit remarkable morphological diversity. This study compares Lean and Siscowet ecotypes to understand genetic and epigenetic underpinnings of their phenotypic differences.
High-fidelity long-read sequencing enables detection of structural variants and native DNA methylation simultaneously, providing comprehensive genomic insights.
All data, code, and analyses are publicly available on GitHub. This browser is deployed via GitHub Pages for easy access and reproducibility.
| 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 |