Sentence examples for base in the read from inspiring English sources
As described, the first four bases are index sequences for library discrimination, and therefore the actual tag sequence starts at the fifth base in the read and terminates at the anchoring restriction enzyme sites (NlaIII, DpnII or BfaI; Figure 1, bottom).
In this step, reads having more than 5 bases with a quality score below 10 (PHRED score) [12] and reads with sequence entropy below 0.85 were removed (where entropy was calculated by summing -p*log2(p) for each of the four bases; p is the frequency of a base in the read).
Intercept: The quality of the first base in the read.
The cycle covariate corrects the qualities based on the position of the base in the read.
2. Reads that mapped off-target, so that no base in the read was aligned to a targeted exon base pair, were discarded.
For these reasons, we fit a linear regression model to each read's quality scores and use the regression parameters as features for classification: Intercept: The quality of the first base in the read.
To assess the quality of RNA-seq data, each base in the reads was assigned a quality score (Q) by a phred-like algorithm using the FastQC [ 38].
For 100 bp reads, sequence divergence had almost no effect on the mapping accuracy, even if up to 9% of the bases in the read were mutated.
In this state, we expect that most bases in the read match their partner in the genome, and that the probability of matching will vary based on the read base quality (high quality bases are less likely to be sequencing errors and thus more likely to match).
An index is defined by a spaced seed (or mask), a string of 0s and 1s that start and end with a 1, that define the bases in the read considered during the lookup in the index (see Table 1 for a complete example optimized for the human genome).
