Sentence examples for mapping qualities of from inspiring English sources
SNP calls should have been present in at least 10 reads, with SNP mapping qualities of the bases higher than 20.
Reads that map equally well at multiple locations or fail to map at all are given mapping qualities of 0. For many experiments, alignments below a certain mapping quality, usually values of 20, 30 or 40, are filtered out.
The second models nucleotide and mapping qualities of the reads by probabilistically weighting the contribution of a read/nucleotide to the inference of a SNV based on the confidence we have in the base call and the read alignment.
In fact, SOAP only reports mapping qualities of 0 or 30, and all quality-30 mappings are at the top of the red line (precision≈ 0.5) with all quality-0 mappings represented as an invisible blue dot under the red line at precision 0.45.
First, single nucleotide polymorphisms (SNPs) were called for each sample individually using SAMtools v.0.0.18 mpileup function [ 55], filtering by base and mapping qualities of at least 20.
For in-house genomes, SNP calls were then made by using SolSNP version 1.1 with the following alignment limits: minimum coverage of 20, minimum mapping qualities of 20, and a filter call of 0.95.
To get RNA-seq quality metrics, bedtools utility (http://bedtools.readthedocs.org) was used to overlap TopHat2 mappings with mapping quality of at least 20 and defined exons and introns with a minimum overlap fraction of.8.
Only uniquely-mapped reads were retained for subsequent analyses (mapping quality of at least 20 and perfect matches) (Li et al. 2009).
Alignment was performed with BLASR28 -bestn 3, and primary aligned reads with mapping quality of 254 were used.
The alternative mapping quality of a predicted SV is the average mapping quality calculated over discordantly mapping read pairs within a cluster.
Similar to GATK [ 18], only the mapped short reads with mapping quality of greater than 20 were considered, and only bases with base quality greater than 17 counted.
