Sentence examples for mapping quality value from inspiring English sources

Secondly, read pairs where one mate is aligned to the genome reference uniquely (i.e. with high read mapping quality value, or MQ) and the other mate is either soft-clipped or unaligned, are collected as the starting material for SR mapping.

A pile up alignment file of all uniquely mapped reads with a mapping quality value of ≥20 was generated using SAMtools v1.8 (Li et al. 2009).

Alignments with a MAPping Quality value >10 were considered as valid.

Buffer distance was set at 1000 bp in this work, and clusters with a minimum of 25 piece-alignments and a minimum average Phred-scale mapping quality value of 150 were subjected to further examination for detection of candidate breakpoints.

As the PacBio pipeline doesn't generate a mapping quality value and to ensure a fair comparison, we remapped the reads of all technologies using the k-mer based mapper, SMALT [ 9], and then analysed coverage across the P. falciparum genome (Additional file 3: Table S4).

The remaining sites had reads spanning the SNP position with mapping quality values of zero and not called.

Platform-specific error rates are modelled as priors and mapping quality values from the mapper are incorporated as part of the data.

The "mpileup" function in SAMtools software [ 42] was used to detect the SNPs between the Zhongzhi No. 13 and ZZM2748 parental lines using reads with mapping quality values greater than or equal to 20.

In this section, we describe the full VARiD variation identification algorithm, including the expanded HMM utilized to address the above shortcomings, and the use of base and mapping quality values to parameterize the emission probabilities.

The sensitivity and genotype concordance numbers for the chr12 capture array were not as high, but the loss of sensitivity can be explained by lack of evidence of the alternate allele in the read pileup or poor zero mapping quality values spanning the SNP position.

This framework also provides better dynamic range than the raw mapping quality values provided by most tools, suggesting that it may be valuable for researchers who desire more granularity in their data analysis.