📊 Transposon Analysis: Sequencing Depth Requirements

🔬 Purpose of Analysis

• Tn-seq / TraDIS / INSeq
  Used for mapping transposon insertion sites across the genome.
  Recommended coverage: 500× to 1000×

• Native transposon (IS) detection
  Detects existing mobile genetic elements such as insertion sequences (IS) or integrons.
  Recommended coverage: 30× to 50×

• Structural variant (SV) or mobility analysis
  Identifies large insertions, deletions, or mobile element insertions.
  Recommended coverage: at least 50×

• Abundance or fitness estimation
  Quantifies insertion events under different experimental conditions.
  Recommended coverage: 200× to 300×

• Long-read mobile element assembly
  Uses technologies like Oxford Nanopore (ONT) or PacBio to resolve repetitive mobile elements.
  Recommended coverage: 20× to 30×

🧬 Your Data (Example Samples)

• Sample 1
  Total bases: 2.0 Gbp
  Mean read length: 8,635 bp
  Estimated read count: ~233,000
  Approximate genome coverage: ~500×

• Sample 2
  Total bases: 2.5 Gbp
  Mean read length: 6,851 bp
  Estimated read count: ~366,000
  Approximate genome coverage: ~625×

• Sample 8
  Total bases: 1.26 Gbp
  Mean read length: 5,180 bp
  Estimated read count: ~243,000
  Approximate genome coverage: ~250×

• Sample WT
  Total bases: 1.88 Gbp
  Mean read length: 10,910 bp
  Estimated read count: ~172,000
  Approximate genome coverage: ~600×

Assuming an average bacterial genome size of ~4 Mb

✅ Conclusion

• Your sequencing depth ranges from 250× to 625×, which is:
• Ideal for transposon insertion site mapping
• Suitable for detecting low-abundance or rare insertion events

• Adequate for native mobile element discovery

• If your goal is Tn-seq, your current data provides excellent coverage for both insertion site resolution and abundance profiling.

📊 Recommended Sequencing Depths for Transposon Analysis

• Tn-seq / TraDIS: Recommended depth is 500× to 1000×.
  This high depth is necessary to ensure adequate coverage across insertion sites and to detect low-frequency transposon insertions.

• Detection of native insertion sequences (IS) / mobile elements: A depth of 30× to 50× is generally sufficient.
  This enables reliable identification of naturally occurring transposable elements in bacterial genomes.

• Structural variants (SVs) and comparative genomics: Aim for more than 50× coverage.
  Higher coverage improves confidence in detecting large insertions, deletions, or rearrangements during comparative analysis.

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