Sentence examples for base quality values for from inspiring English sources
PolyBayes can use individual base quality values for the calculation of SNP probabilities, but because original chromatogram data is not available for all sequences, we have assigned arbitrary base quality values to these sequences.
These arbitrary quality values were derived based on the estimated sequencing error rate for the different types of sequences used: EST sequences were assigned an arbitrary base quality value of 20 (1 error per 100 bases), which is typical for single-pass, unedited sequences; while sequences derived from individual submissions to GenBank were assigned a quality value of 30 (1 error per 1000 bases).
Polybayes likely suffered from the relatively large number of ESTs obtained in GeneBank for which no base quality values were available.
PHRED software [ 65] was used for base calling and assignment of base quality values, and vector and low quality-sequences were removed from the reads on the Egene platform [ 66].
Although it is possible to use base quality values to discern true allelic variations from sequencing errors, validation is a key step for detection of true SNPs [ 15].
Furthermore, in seed selection stage, sequencing base quality value will be used to avoid the risk of picking seed with errors, especially for seed of nonrepeats.
Figure 1 shows a base-call graph for the dataset, and Figure 2 shows the accompanying quality values for these base calls.
Vector sequences were filtered automatically and low-quality bases (quality value <20) were removed.
The sequencing data were stored in FASTQ format, which provides information on the sequence identifier, read sequence and quality values for each base.
To further assess the quality of the sequence around/in each SNP we used a statistical software package (PolyBayes [ 34]) together with quality values for each base that were derived from the expected error rate for each sequence (described in Methods).
(B) Histogram of modification quality values for all bases.
