In these cases, a consensus sequence required a minimum of three independent EST sequences across all regions of the consensus.
Shotgun sequence reads from the Lib35k library were mapped onto the mitochondrial consensus sequence using BlastN (minimum length of 400 bp and at least 90% sequence identity).
All PCR were repeated two to four times independently from the same DNA to reduce the number of wrong base pairs in the final consensus sequence to a minimum due to errors produced by Taq polymerase.
All PCR reactions were repeated two to four times independently with the same individual to reduce errors, possibly created by the Taq polymerase, in the final consensus sequence to a minimum.
Based on this analysis, a minimum of six changes from the mtDNA consensus sequence would be expected in a read from a pseudogene with our MT-CO3 primers and ∼48 changes for the MT-HV2 primers.
For each spruce consensus sequence, the blastx hits with a minimum similarity value of 0.75 and a minimum coverage of 0.5 were used in the GO assignment procedure.
To meet our sequence quality criteria, the resulting clone consensus sequence was required to achieve a minimum average score of Phred35, with each base position having a minimum score of Phred30.
To meet our hq criteria, the resulting clone consensus sequence was required to achieve a minimum average score of Phred35, with each base position having a minimum score of Phred30.
If given a consensus sequence to evaluate, computing the minimum number of crossovers to support it with haplotype regions.
Each base position also required at least two sequence reads, of minimum Phred20, that were in agreement with the consensus sequence (i.e., no high-quality discrepancies).
