Question: Differences of taxid and species_taxid in assembly_summary.txt
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gravatar for xieshaojun0621
11 months ago by
United States
xieshaojun0621130 wrote:

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

ncbi refseq assembly genome • 264 views
ADD COMMENTlink written 11 months ago by xieshaojun0621130

40324 - gives you all Stenotrophomonas species.
391008 - gives you the specific strain.

561 is Escherichia spp
562 is Escherichia coli but those appear to be used interchangeably in that file.
You can check using the NCBI Taxonomy browser here.

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax69k
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