Possible causes of antibiotic resistance of E. coli to ampicillin (Supplementary materials)

Table 2

Pictures

Raw sequencing data

Reference sequence of non-mutated E. coli: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/ (We need sequence in fasta format (GCF_000005845.2_ASM584v2_genomic.fna.gz) and annotation in .gff format(*_genomic.gff.gz). This is E.coli strain K-12 substrain MG1655, laboratory workhorse.)

Raw Illumina sequencing reads from shotgun sequencing of an E. coli strain that is resistant to the antibiotic ampicillin: https://doi.org/10.6084/m9.figshare.10006541.v3 (1 and 2 refer to forward and reverse, this was a paired end run).

Lab Notebook

Laboratory Notebook, which is made as a Jupyter Notebook, is uploaded directly in this repository. All the necessary commands and data processing is listed there. To recreate the results, one should simply download the raw data and run the notebook.

FastQC reports (before and after trimming)

Can be found in corresponding folder.

VarScan results with mutations