I am a computer engineer and nowadays trying to grasp some concepts of Bioinformatics particularly, reference genomes and genomic variants. My aim is to find the effect of sequence features on variant types that occur in bacteria genomes. I chose Escherichia coli as the bacteria for my study since there seem to be more publication and data about it and its genomic sequences.
When I made a research about variants, I found out that we need to have a reference genome for the comparison with other alleles in order to find variants. And, I even read that we can use genomic sequence of one bacteria as the reference but it won't represent the cohort in an accurate manner. I got the genomic sequence data for several strains of Escherichia coli bacteria that been sequenced before. However, most of these sequences are not complete ones. I filtered out the complete DNA genomes. When I checked the reports on these genomes, I learned that these are complete genomes but not reference genomes. Only the ones which have
RefSeq category: Reference Genome in their report are reference genomes for Escherichia coli.
Learning that most of the data I got for different strains of Escherichia coli were not reference genomes, I tried to seek to find reference genomes and I got this website of NCBI ref sequences for prokaryotes. This website shows only two reference sequences which match with what I have find in all sequencing data I got before. So, I want to ask two questions
First: How can I get a reference sequence for other strains of E. coli?
Second: If I cannot get a reference sequence for other strains, can I use complete genome data as the reference one? When I check the complete genome data, I cannot understand their order because there are other data for same strains that show loci of sequences but in the complete genome, I cannot see any order of the loci. Even, I cannot see data of some loci in the complete genome which blows my mind more.
I know it may not be appropriate to ask two questions in a single post, however, these two questions seem to support each other. I will appreciate any of your help.