Based on a similarity cut-off of 97%, the minimum Good's coverage value was 0.95, meaning that a sufficient number of reads were obtained to evaluate bacterial diversity.
We picked minimum coverage and identity values (50 and 40%% respectively) which are significant enough to establish an evolutionary relationship between two protein sequences.
Potential nucleotide variants should be greater than the sequence quality value (QV), neighbour quality value (NQV), minimum coverage (MC), and minimum minor allele frequency (MMAF).
Initial parameter values were: minimum coverage depth 3, minimum SNP quality 20, minimum indel quality 50, with other parameters such as window size and nearby SNP and gap density left at their defaults.
If your policy provides minimum coverage, you may need to compute the value of the loss or damage of a newer vehicle (the rental car) and decide if you need to supplement your coverage.
Varscan 2.3 [ 27] was used to detect Single Nucleotide Changes SNC) and InDels from alignment results with minimum coverage of three reads and a p-value cutoff of 0.1.
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.
Daucus protein sequences greater than 33 amino acids available in GenBank were used for blast (TBLASTX) analysis against our EST collection, using a cutoff value of e-05 and minimum coverage length ≥100 nt.
Assembled sequences were used for blast searches and annotation against the NCBI nr database using a cutoff e-value of e-05 and minimum coverage length ≥33aa.
For M. smegmatis, homologues for the 27 genes in the Sharp and Li data set were identified through reciprocal BLASTP, enforcing a maximum e-value of 10−3 and a minimum coverage of 40% positives on all BLASTP searches.
