Here is a snippet of a kraken2 report.
0.74 605528 0 O 85011 Streptomycetales
0.74 605528 10003 F 2062 Streptomycetaceae
0.71 581926 131552 G 1883 Streptomyces
0.21 168546 40902 G1 2593676 unclassified Streptomyces
0.01 9744 9744 S 2005885 Streptomyces sp. S063
0.01 8561 8561 S 2742137 Streptomyces sp. NA02950
0.01 4360 4360 S 2609808 Streptomyces sp. LBUM 1480
0.01 4137 4137 S 659352 Streptomyces sp. SN-593
0.00 3867 3867 S 2078691 Streptomyces sp. CB01881
0.00 3086 3086 S 2175864 Streptomyces sp. NHF165
0.00 3077 3077 S 2721244 Streptomyces sp. RPA4-2
0.00 2753 2753 S 2136173 Streptomyces sp. So13.3
0.00 2656 2656 S 1972846 Streptomyces sp. Sge12
I am not understanding my there are reads classified as Streptomyces and to "unclassified" Streptomyces. I can't find information on this in the kraken2 wiki.
Once guess might be that if there were an entry in the kraken2 database that were classified only to the genus level (taxon 1883, then reads could be assigned to that. However, all of the Streptomyces entries in the database are to the species or strain level.
Any ideas?
1 answer
It has to do with the structure of the NCBI taxonomy. Many entries in the taxonomy are Streptomyces something or other, having their taxonomic parent as "Unclassified Streptomyces" (taxid 2593676), rather than the genus Streptomyces (taxid 1883). The taxonomic parent of 2593676 is 1883. I don't know the reason for the extra layer, but in the above example G1 is indented under G so the G1 counts are included in the G counts. So probably nothing to worry about, unless taxonomic divisions not based on phylogenetics disturb you, which they should.
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