SNP23: Analyzing the genomic differences between wild type strains (as published in reference genomes) and strains kept under lab conditions (resequenced by the Segrè lab in 2019)

❓Questions we are trying to answer:

What are the SNPs in the re-sequenced genomes (vs original genomes? I.e., how many SNAPs/genome, location of SNPs, what genes are affected?
What are other genomic changes compared with the original genome? E.g, rearrangements, paralogs.
Is there conservancy in the number of SNPs based on phylogenetic relationships? I.e Do closely-related microbes undergo similar changes?

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results		results
.gitignore		.gitignore
README.md		README.md
metafile.csv		metafile.csv
mini_metafile.csv		mini_metafile.csv
reads_to_vcf.out		reads_to_vcf.out
reads_to_vcf.sh		reads_to_vcf.sh