AssayMutRatio           Calculate the mutation detection rate using
                        different assays
LastfiveNrMutation      Bacth assay analysis for last five Nr of
                        primers
MutByGene               Plot mutation counts for certain genes
assays                  Assays for mutation detection using different
                        primers and probes
chinalist               A list of places in China
covid_annot             Mutation annotation results produced by
                        "indelSNP" function
doubleAssay             Detection of co-occurring mutations using
                        double-assay information
gene_position           "GFF3" format gene position data for SARS-Cov-2
gff3                    "GFF3" format annotation data for SARS-Cov-2
globalProteinMut        Global mutational events profiling of proteins
globalSNPprofile        Global single nucleotide polymorphism (SNP)
                        profiling in virus genome
indelSNP                Provide effects of each single nucleotide
                        polymorphism (SNP), insertion and deletion in
                        virus genome
mergeEvents             Merge neighboring events of single nucleotide
                        polymorphism (SNP), insertion and deletion.
mutStat                 Plot mutation statistics for nucleiotide
nucmer                  Mutation information derived from "nucmer" SNP
                        analysis
nucmerRMD               Preprocess "nucmer" object to add group
                        information
nucmerr                 Preprocessed "nucmer.snps" file using
                        "nucmerRMD" function
plotMutAnno             Plot the mutation statistics after annotating
                        the "nucmer" object by "indelSNP" function
plotMutProteins         Plot the most frequent mutational events for
                        proteins in the SARS-CoV-2 genome
refseq                  SARS-Cov-2 genomic reference sequence from NCBI
