An estimate of large-scale sequencing accuracy

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Estimating DNA sequencing accuracy typically requires redundant sequencing efforts.
• Public DNA databases may contain contaminations from cloning procedures.
• Mobile genetic elements can complicate sequence analysis.

Purpose of the Study:

• To assess the accuracy of large-scale DNA sequencing.
• To identify and address potential sources of error or contamination in public databases.
• To establish a reliable method for estimating sequencing error rates.

Main Methods:

• Utilized the IS10 mobile genetic element, a component of the transposon Tn10, as a reference.
• Analyzed sequence variation within IS10 across multiple clones.
• Compared observed variations against known IS10 sequence data.

Main Results:

• Identified significant contamination in public databases by the IS10 element due to its use in bacterial cloning strains.
• Determined the natural range of sequence variation within IS10.
• Established that the DNA sequencing error rate is very low, likely less than one error per ten thousand bases.

Conclusions:

• The IS10 element's presence in databases requires annotation as contamination.
• The low observed error rate suggests high accuracy in current large-scale DNA sequencing technologies.
• Defining sequence variation in mobile elements provides a robust method for error rate estimation.