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False positives detected during the SNP discovery as a result of sequencing errors should have increased the number of transversions relative to the number of transitions.
Our genome sequences are lacking coverage of several PE-PGRS genes most likely as a result of sequencing bias due to high GC-content in those genes.
To minimize the possibility of misidentifying samples as a result of sequencing or adapter synthesis error, all pair-wise combinations of barcodes differed by a minimum of three mutational steps.
Not unexpectedly, divergence estimates increased drastically with low BQ as a result of sequencing errors.
Some of these substitutions may have occurred as a result of sequencing errors or site-specific polymorphism within each species.
In an attempt to exclude potentially spurious tags, generated as a result of sequencing errors, only tags that were observed more than once were included.
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Heteroplasmic-like patterns frequently show up in the electropherograms as a result of sequence background noise.
Homolog identification can be difficult when comparing genomes across great evolutionary time as a result of sequence evolution and paralogous duplication events within a lineage.
For example, a probe might hybridize to only one paralog in one species but to both paralogs of genes in another species, either as a result of sequence divergence or because both are expressed in one but not the other.
Coding mutations will also reduce the detection of viral peptides as a result of sequence variability among strains [ 47, 48].
The cp genomes could provide valuable information for taxonomic classification and the reconstruction of phylogeny as a result of sequence divergence between plant species and individuals.
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