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Astericks indicate short CDS that may be gene calling error.
Somewhat surprisingly, SVDetect has an increasingly better performance as the base calling error increases.
Therefore, we take the variant calling error rate to be on the order of ε = 0.05.
Each NGS technology displayed some intrinsic properties, i.e. base calling error, systematic bias, etc.
The same method was used to count INDEL errors and single-base substitutions and to calculate variant calling error rates.
The paired-end 36 bp reads were filtered based on their Phred scores [ 15], using a cutoff of 30 [ 16] which indicates a base calling error of 0.001.
Similar(36)
This measure pSNP quantifies base calling errors and SNP calling errors [49].
Call clustering was inspected manually and adjusted when obvious calling errors were made by the software.
Resulting chromatograms were manually trimmed and checked for calling errors.
Genotype calling was simulated by adding sequencing and calling errors at frequencies representative of NGS data.
Other efforts have been made to understand the sources of variant calling errors [ 12].
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