Differences of taxid and species_taxid in assembly_summary.txt
In the file I downloaded here (ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt ), there are two columns: taxid and species_taxid
What's the difference between these two columns?
Some of the lines these two columns are different: 391008 40324 Stenotrophomonas maltophilia R551-3
Some of them they are the same: 562 562 Escherichia coli
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40324- gives you allStenotrophomonasspecies.391008- gives you the specific strain.561isEscherichiaspp562isEscherichia colibut those appear to be used interchangeably in that file.You can check using the NCBI Taxonomy browser here.