Supplemental Material for Chhotaray et al., 2019
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
Supplementary sheet 1 contains details of Illumina sequencing library preparations and Bioinformatics analysis of sequencing data. Figure S1 contains the KEGG Classification annotation statistics of MabS and MabR whereas Figure S2 contains the COG classification annotation statistics of MabS and MabR. Figure S3 and Figure S4 contain the pan-genome and core genome phylogeny of 25 complete genome sequences of M. abscessus species respectively. Figure S5 contains gelelectrophoresis of plasmids extracted from M. abscessus clinical strains. Figure S6 contains the maps representing the circular visualization of insertions and deletions in MabR (CP034191) and MabS (CP034181). Table S1 contains the annotations and related data for linear plasmid pMabS_GZ002 gene. Table S2 contains the information about the variation in methylation sites in the genes of interest between two clinical strains of M. abscessus. Table S3.1, Table S3.2, and Table S3.2, contain the information about the gene content in the inserted and deleted regions (Reference vs MabR), (Reference vs MabS), (MabS vs MabR), respectively. Table S4 contains the information about the drug susceptibility of M. abscessus isolates. Table S5 contains statistics of PF data generated by Illumina sequencing. Table S6 contains the statistics of clean data after quality control. Table S7 contains the proportion of statistics of the clean data compared to PF data after quality control. Table S8 contains the genome alignment statistics of two M. abscessus clinical strains obtained from Illumina sequencing. Table S9 contains the raw reads statistics of two of M. abscessus clinical strains generated from single molecule Real-Time (SMRT) sequencing. Table S10 contains the genome assembly statistics of two M. abscessus clinical strains obtained from single molecule Real-Time (SMRT) sequencing. File Xls S1 contains result of structural variation analysis. File Xls S2 contains the information about the identified SNVs, each motif’s methylation site, methylation score, type of methylation, and all locations of discovered motifs in strains, motif information of pMabS_GZ002 plasmid, identified methyltransferase in both strains. File Xls S3 contains the statistics of the 25 available complete genomes of M. abscessus used for pan-genome analysis. File Xls S4 contains the statistics number of accessory genes, unique genes as well as exclusively absent genes determined among the M. abscessus species. MabS.h5 and MabR.h5 contain the raw files of methylome analysis of MabS and MabR.h5, respectively.