Sentence examples for maximum read depth from inspiring English sources
All SNPs with maximum read depth less than 100 were kept for subsequent analysis.
Default settings were used, except that the maximum read depth was set to 400X (−D400X.
Brain tissue sample read depths varied from RV50, total viral reads 293, maximum read depth 16, and average read depth of 8.6; to RV437, total viral reads 1,489, maximum read depth 103, and average read depth of 44.
To minimize the number of false positives due to paralogues sequences, a maximum read depth of 4 times the average read depth was used.
SNPs were called only for positions with a minimal mapping quality (-Q) of 20, and maximum read depth (-D) was set at 200.
The resulting pileup file was further processed by the bcftools and vcfutils varFilter.pl programs of the SAMtools package allowing a maximum read depth of 200.
Read depths from cell cultured viral samples were higher, with average read depths of 31 (RV20 depleted), 125 (RV20) and 65 (RV2324 cell pellet) and maximum read depths of 69 (RV20 depleted), 228 (RV20) and 272 (RV2324 cell pellet).
Briefly, we mapped the wMelCS reads to the reference wMel genome using BWA (Li and Durbin 2009), then generated a pileup file with minimum and maximum read depths set to 10 and 100, respectively, and converted the resulting fastq file to fasta format.
SNP calling was done in iterations starting with maximum global quality 999 (phred-scaled quality score for the assertion. -10log_10 prob), minimum read depth of 15x, and absence of other SNPs in 50 bp flanking regions.
Blue numbers above each point show the number of sites that fall within the decile; purple numbers below each point show the maximum total read depth for that decile (minimum total read depth is the maximum depth for the previous decile, or 300 for the lowest decile).
Of the 75 samples with less than optimal DNA input, 32 samples still generated the maximum possible coverage of approximately 97%, and a further 20 samples generated a coverage of >95% at a minimum read depth of 100x.
