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Question: Differences of taxid and species_taxid in assembly_summary.txt
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Entering edit mode
16 months ago
xieshaojun0621 • 120
United States

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

Entering edit mode
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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 16 months ago
genomax
68k

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