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Coverage Formula:
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The Illumina coverage calculation estimates sequencing depth by determining how many times each base in the genome is sequenced on average. It's a critical metric in genomics research to ensure sufficient data quality for variant calling and analysis.
The calculator uses the coverage formula:
Where:
Explanation: The equation calculates the total number of bases sequenced and divides by the genome size to determine how many times each base is covered on average.
Details: Proper coverage estimation is essential for designing sequencing experiments, ensuring sufficient data quality for downstream analysis, and optimizing sequencing costs while maintaining research quality standards.
Tips: Enter genome size in base pairs, read length in base pairs, and the number of reads. All values must be valid positive numbers.
Q1: What is considered good coverage for Illumina sequencing?
A: Coverage requirements vary by application: 30-50x for whole genome sequencing, 100x+ for exome sequencing, and higher for detecting rare variants.
Q2: How does read length affect coverage?
A: Longer reads provide more contiguous coverage but may have higher error rates toward the end. Shorter reads are more accurate but provide less context.
Q3: Does this calculation account for sequencing errors?
A: No, this is a theoretical calculation. Actual effective coverage will be lower due to sequencing errors, PCR duplicates, and alignment issues.
Q4: How does library preparation affect coverage?
A: Library preparation quality significantly impacts coverage uniformity. Poor library prep can lead to coverage biases and gaps in the data.
Q5: Can I use this for other sequencing platforms?
A: While the formula is universal, different platforms may have different error profiles and read characteristics that affect actual coverage quality.