theory.toys – Read Simulator

Sequencing Parameters

Reference Length: 100 bp Read Length: 50 bp Coverage: 10x

Error Model

Base Error Rate: 1.0% Position-Dependent Errors: (Higher errors at read ends) Indel Rate (% of errors): 10%

Display Options

View Mode: 🔑 Unlock

Max Reads to Display: 20

Sequencing Statistics

About Sequencing Errors

Phred Quality Scores: DNA sequencing produces short reads with position-dependent errors. Quality scores encode error probability: Q = -10 log₁₀(P). Common values: Q10 = 10% error, Q20 = 1% error, Q30 = 0.1% error.

Error Types: Substitutions (A→C), insertions, deletions (indels). Illumina reads typically have higher error rates at read ends due to signal decay.

Coverage: Number of reads covering each position follows Poisson distribution. Higher coverage improves variant calling accuracy.