Sentence examples for base in the reference from inspiring English sources
We then mapped these reads to the reference genome using Pash 3.0 [22] and created a comprehensive methylation map, where each cytosine base in the reference genome is annotated with the number of times methylation is observed at that position.
In addition, any putative SNPs in low-coverage sites where the majority base differed from the reference genome but the majority consisted of only 1 or 2 bases were rejected due to lack of sufficient data, and replaced with the base in the reference genome.
Each base in the reference genomes was further classified as coding or non-coding based on Ensembl genome annotation [ 31] (drosophila melanogaster_core_37_4e, and homo sapiens core_45_36g).
A base in the reference was considered to be incorrect if at least a minimum of 10 reads scored the nucleotide differently (with both DNAseq and RNAseq).
To be precise about terminology, we term any base that differs from the consensus base (typically the base in the reference genome) a single nucleotide difference (SND).
In general, if a base in the reference sequence has a high enough coverage with a consistent difference from its reference, this base likely represents a polymorphism.
First, we enumerated all exact sequence repeats of ≥36 bases in the reference genome using MUMmer (version 3.23) [ 35].
For each alignment, the identity level was computed as the fraction of bases in the reference sequence that are paired with identical bases in the target sequence.
The overlapping factor is calculated by the software from the two different bases in the reference and sample traces on either side of the mutation.
Enforcing the inclusion of at least one sequence of at least 1400 bases in the reference set improved results at identity thresholds lower than 0.9 visibly (Fig. S5).
