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SR methods require multiple reads to support an event at (nearly) a single nucleotide location.
While these polymorphisms were supported by the sequences of multiple reads, to ensure their accuracy we also subjected a group to testing by q-PCR and high resolution melting (HRM) analysis (Table 2).
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Pyrosequencing is often limited to shorter reads (approximately 100 bp) requiring multiple tiled reads to achieve the coverage observed with BSAS [ 14].
Not surprisingly, the largest factor for this range in validation was due to the use of one versus multiple short reads to predict a SNP.
We used consensus sequences from multiple clone reads to sort true nucleotide polymorphisms from Taq polymerase error in incorporated PCR fragments.
Multiple reads mapping to the same position were counted only once to remove potential bias from PCR.
If multiple reads mapped to the same genomic location, only one was kept to avoid amplification bias.
Manual inspection of the mapping results revealed five merged loci that had multiple reads mapping to a single position near the collapsed locus and to a different scaffold.
Moreover, because RNA-Seq technology can generate multiple reads corresponding to each transcribed nucleotide on the genome, it is usually possible to identify 5' and 3' transcript ends with high resolution [ 15].
In addition, multiple reads matched to uncharacterized positions on 59 different primary miRNA sequences.
Multiple reads mapping to the same position were regarded as PCR duplicates, and only one of them was kept.
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