We attribute this seeming discrepancy to pyrosequencing errors [42], [43] and inaccuracies in sequence alignment, both of which would generally depress all pairwise similarity scores, yet likely preserve the identity of the true nearest neighbor sequence in this type of analysis.
Early studies in which investigators reported apparent signals of recombination in human mtDNA (Awadalla et al. 1999; Eyre-Walker et al. 1999; Hagelberg et al. 1999) were largely discounted by statistical arguments (Innan and Nordborg 2002; Jorde and Bamshad 2000; Kumar et al. 2000) and inaccuracies in sequence data (Hagelberg et al. 2000; Kivisild and Villems 2000).
Due to genetic variability on the one hand, and possible inaccuracies in sequencing and multiple alignment on the other, positions selected for a significant strong (weak) folding in different genomes may be shifted one with respect to the other.
It may be due to an inaccuracy in sequence assembly from the scaffold.
In the event that filtering out too many or too few signal peaks can lead to inaccuracy in sequence determination, the percentage of amino acid residues in the correct positions relative to the total number of amino acid residues in the correct sequence was also calculated for each sequence determined.
We speculate that, beside pyrosequencing errors due to inaccuracies in the sequencing process, also errors from the PCR library preparation step could account for a high percentage of observed errors.
There are several factors that account for erroneous base calls or reads, especially inaccuracies in the sequencing chemistry, leading to slightly too high or low flow values, and carry-forward and incomplete extension errors (Margulies et al., 2005), accumulating over the read, which reflects the stochastic nature of the base incorporation chemistry.
Despite the availability of the draft B73 genome sequences, incompleteness and inaccuracy in genome/BAC sequencing or gene annotations remain problematic for eQTL analysis.
Assembly errors include erroneous copy numbers of repeated genes, errors in gene and chromosomal order, as well as inaccuracies in the actual sequence of individual genes due to the mixing of reads from different repeat copies.
This small number of LD blocks might be due to the distance between SNPs with significant effects or to local inaccuracies in the published sequence or to the presence of limited LD between adjacent SNPs in our population.
At some microsatellites, all repeat number genotypes were non-integer and had a common decimal fraction (e.g. for a tetranucleotide repeat unit all genotypes had a decimal fraction of 0.75), potentially reflecting small inaccuracies in the reference sequences or genotype calls.
