Sentence examples for minimum consensus quality from inspiring English sources

SNPs were filtered using maq.pl SNPfilter with minimum read depth (-d) of 20, minimum consensus quality (-q) of 20, and minimum adjacent consensus quality (-n) of 20.

The SNP filtering was performed using the default parameters except for the minimum consensus quality for SNPs (-q 40).

We used the cns.final.snp output file with minimum read depth of 3 and minimum consensus quality of 30 required to call a SNP for these analyses.

The minimum consensus quality (phred scaled likelihood of the consensus base being incorrectly called) and depth filters minimize the likelihood that random sequencing errors lead to false positive SNP calls.

We filtered the MAQ [ 30] SNP output according to several rules: minimal map quality per read: 10; minimal map quality of the best mapping read on a SNP position: 10; maximum read depth at the SNP position: four times the actual coverage after quality filtering; minimum consensus quality: 10 [ 22].

To call a difference, a minimum MAQ consensus quality score of 30 and read depth of 4 were required at each chromosomal position for both strains.

The Maq analysis method, when used with selected parameters (minimum consensus-base quality of 20, unique read placement; details in Materials and Methods), produced a total of 25,047 predicted SNPs, each predicted using one or more short sequence reads aligned to one position within the genome.

Valid variants had to be seen in both directions with at least 3× coverage and their calling was done using Samtools; minimum mapping quality was 25, consensus quality was 20 and minimum SNV (single nucleotide variation)/indel quality was 20.

Additional sequences were added until a completely contiguous consensus was created representing the entire plastid genome with a minimum of 2X coverage and a consensus quality score of Q40 or greater.

Given the requirements of consensus quality scores of 30 or better, a minimum of 15 × coverage in highly inbred strains, and full resolution of all three codon positions in every strain (including the outgroup), sequencing error alone does not explain the high proportion of singletons observed.

For our analysis of all combined reads (ABC), we generated a mutation list by setting the following cutoffs: an allele frequency between 0.2 and 0.8, a minimum read depth of 4, average hits ≤1, and a MAQ consensus quality score of 40.