A significant P-value indicates that this location may be a consistent mismatch location.
For a given base pair location in the genome, if the number of aligned fragments that carry an allele different from the reference genome is much higher than the expected number owing to random sequencing errors, we call it a consistent mismatch location.
We also compared the Infinium 450K data to reduced representation bisulfite sequencing data generated on the same samples and found a high level of concordance between the two independent methodologies, which can be further improved by filtering for probe sequence identity and mismatch location.
To standardize conventions, alignments and mismatch locations were relabeled relative to the 5' strand of the chromosome.
This process continues until no more consistent mismatch locations are found.
To find all consistent mismatch locations, we first need to estimate the sequencing error rate.
The concept of consistent mismatch and the method to find consistent mismatch locations across the genome are described in Appendix 1.
All features except the number of consistent mismatch locations are straightforwardly calculated: features NE and NI are directly collected from the assembler's output, and NR, MF, MR and CM are calculated by our sharing graph generator.
However, if the reads are misaligned during the first step (e.g. reads spanning a mutation), incorrect mismatch locations will be propagated to the second step, which can bias the study results and lead to questionable conclusions, especially for a large study involving thousands of genomes (DePristo et al., 2011).
The biochips could resolve a mixture of fully complementary five base-pair mismatched targets by the location of binding on the surface.
Per-position mismatch rate is the fraction of overlapping read pairs that are mismatched at any given location in the genome.
