More complex models, including sequence-specific or site-specific error rates, can readily be derived by the same approach.
The method for allele-frequency estimation is efficient in terms of computational speed, allows for site-specific error rates, and yields estimates that are unbiased with minimal sampling variance (within the bounds dictated by the sampling scheme).
The mean site-specific error rate (measured as the count of a non-reference nucleotide divided by total sequencing depth at that position) of the wolverine individual sequenced at high depth was 0.11%, with a range between 0.028% and 2.45%.
We recognize that accurate sequence alignment plays an important role in site-specific error rates, but we anticipate that as technology moves toward larger numbers of concurrently sequenced base pairs, sequence alignment should be a decreasing source of site-specific errors.
High-rate (>1 Hz) GPS, currently used for measurement of dynamic processes and as a universal time and frequency standard, is usually assumed to be affected by site-specific errors and only limited studies of the error properties of high-frequency (10 Hz), short-duration (<100 s) GPS records exist.
There was a negative correlation between sequencing coverage and site specific sequencing error rate (rS = −0.083, df = 15,786, p < < 0.001).
Thus, geometrical isomerism of the AFB1 FAPY formamide group is modulated not only by DNA sequence but also by specific interactions within the active sites of specific error-prone bypass polymerases.
SSE are likely to bias estimates of sequence diversity as they will lead to falsely inferred SNPs in specific error prone sites.
We also found a negative correlation between the site-specific sequencing error rate and coverage, with certain sequence motifs "CCNGCC" being particularly prone to high rates of error and low coverage.
Both −1 frameshifting and stop codon readthrough are site specific and occur at a defined frequency much higher than the background error rates of maintaining the reading frames.
