The median per-base coverage of the input DNA sequence reads was 16-fold, and for the genomic DNA sequence reads was 8-fold, giving a genome-wide ratio of 2. We then ranked all windows from least- to most-covered by input sequence reads, normalized by the genomic read counts.
We calculated the genome-wide, per-base coverage of the S288c genome using SAMtools.
cSNP%: the percentage of non-match base coverage of the total coverage without counting the non-crisp coverage.
Figure 2 shows the base per base coverage of the reads aligned by BLAT for both the PacBio and Illumina datasets across the P. micrantha chloroplast genome, showing a more uniform coverage of genome by the PacBio RS dataset.
The Pearson correlation between the per-base coverage of the forward and reverse strands was calculated, each time shifting the reverse strand by increments of 1 bp (beginning from a lag of 20 up to 5000 bp).
The per-base coverage of the tRNAs was computed and divided by the total number of reads and then multiplied by 100, leading to values that are comparable between samples (percentage).
Base coverage of the C. rosea genome was generated using Illumina HiSeq paired end sequencing with an insert length of 0.5 kb and read length of 100 bp using standard library preparation kits.
Based on these three counts, aligned reads' weight, and reads' base probability, three scores that reflect the likelihood of a SNP at each location in the reference are generated: cSNP%: the percentage of non-match base coverage of the total coverage without counting the non-crisp coverage.
Sophisticated dominator analysis is applied to provide hints on how to generate efficient test cases to increase, as much as possible with as few tests as possible, the control-flow and data-flow-based coverage of the SDL specification being tested.
The admission of all acutely ill patients to the nearest public hospital in their region of residence and the submission of all of the hospitals' BCs to the three clinical microbiology departments prompts population-based coverage of the DACOBAN database.
Suitable BACs were selected based on coverage of the gene of interest and its upstream sequence.
