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We also used male chromosome X haplotypes from the 1000GP samples to simulate sequencing reads with varying insert size, read length, and base error rate.
The algorithm calculated base error probabilities based on their quality values, normalized to a PHRED scale.
The final genome is based on 85,529 reads, with a total coverage of 6.52X (Q20) and overall base error probability 0.26/10 Kb.
Primers CT-C, CT-G, CT-N6, and CT-L were designed based on sequence results to eliminate base error introduced by the first set of primers.
In our 454 data, base error rates were very low.
Not unexpectedly, performance improved with increasing read length and decreasing base error (Table 2).
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