When a nucleotide in a DNA sequence is different from the preceding nucleotide, this is defined as a nucleotide fluctuation.
We focused on the link between intron presence and GC-gradients, analyzing patterns of GC-content variation at different scales from the nucleotide level to the gene scale within each of the two genomes.
For S-cdA, although nearly 1000-fold lefficientient relative to a template A, the correct nucleotide dTMP incorporation was preferred by Dpo4 (Table 6), but the efficiency of misincorporation was not significantly different from the correct nucleotide incorporation in that dGMP, dAMP, and dCMP incorporations were 53%, 29%, and 12%, respectively, as efficient as incorporation of dTMP.
The unconventional intron in A. fumigatus hacA is only 20 nucleotides in length, which is similar to what has been reported in the human homolog but strikingly different from the 252 nucleotide intron in the S. cerevisiae homolog.
When we analyze the bases targeted by ENU we find that 78.6% of mutations are found at A or T. This is quite different from the random nucleotide distribution observed during in vitro culture where 44.5% of the SNVs are at A or T, close to the natural incidence in the genome (45% A or T) [ 55].
We utilize multiple signals to distinguish sequencing errors from real variants: In the absence of a variant, the frequency of the reads with a nucleotide different from the reference base at a particular position should be similar across multiple pools.
In the absence of a variant, the number of reads with a nucleotide different from the reference base should not be significantly greater than that expected based on the sequencing error rate.
In the absence of a variant, the frequency of the reads with a nucleotide different from the reference base at a particular position should be similar across multiple pools.
In case of polymorphisms with a length different from one nucleotide, the 3′ end position of the variant was used.
