Only bins that were sufficiently covered (per base at least a sequence depth of 7x and maximum of approximately 2 x average coverage) were considered.
We were able to cover up to 98% of the targeted bases at a long-read sequence read depth of ≥3, 86% at a read depth of ≥10, and over 50% of all targets were covered with ≥20 reads.
Alkylation occurs at guanine bases with a sequence selectivity similar to other alkylating agents such as the nitrogen mustards.
This region is highly conserved and, based on comparisons at a sequence and structural level, appears to segregate into two groups one containing H1, H2, H5, H6, H8, H9, H11, H12, H13 and H16 subtypes and the other H3, H4, H7, H10, H14 and H15 subtypes.
Data from exome sequencing are typically reported as percent targeted bases sequenced at a given sequencing depth threshold.
We selected SNPs located at least 750 bases away from a sequence contig gap (to make primer design feasible) reducing the number of testable SNPs to 393 of which 348 yielded primers using a primer design package[ 13].
Proactive mechanisms are typically time series based, where a sequence of events at defined intervals are analysed to find patterns that can be used to forecast future values.
The results show that the trimming of low-quality bases at the sequence read ends improved the assembly significantly.
Next, we analysed base changes at a gene sequence level after alignment with BLAST search, by focusing only on protein-coding sequences because one purpose of the analysis was to recognize changes in codon usage.
That is, in cases where both methods assigned a base identity at a particular sequence position, those assignments were always identical (data not shown).
