Escherichia coli Genome sequencing. Escherichia coli

Sequencing samples of 15 Escherichia coli strains were analyzed (the reference genome of Escherichia coli was K-12 substr.MG1655).The analysis included BWA for sequence alignment, Samtools for file processing, and GATK for mutation detection and filtering. It was found that the reference genome of NCBI database was quite different from the sample, and the result was not satisfactory (Annex I). Two samples of Escherichia coli were of very poor quality, so spdaes was used to assemble the sequencing data, pyain analysis and manual selection were followed by S-ECO61 assembly gene (Annex II) group as the reference genome of Escherichia coli.Poor quality E. coli samplesabriacte annotation of resistance genes was performed on the CDS sequence file of E. coli after annotation of reference genome, and genome-wide similarity comparison was conducted for all samples. A total of 128 resistance genes were annotated (Annex III), and the mutation sites of at least 3 of them were selected for annotation. Compared with the sensitive strains of Escherichia coli, a total of 4 mutant resistance genes were found.