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Table 3 Summary of the Genus-level classification for three Human Microbiome Project datasets ( k =20)

From: CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

SRS ID

High confidence

Low confidence

No assignment

Average

Most frequent genera (high

 

assignments (%)

assignments (%)

(%)

confidence score

confidence assignments)

015072

62.3%

25.9%

11.8%

0.868

Lactobacillus (64.7%)

(vagina)

    

Pseudomonas (7.3%)

     

Desulfosporosinus (4.4%)

     

Clostridium (1.7%)

     

Gardnerella (1.2%)

019120

55.1%

28.2%

16.7%

0.842

Streptococcus (27.2%)

(mouth)

    

Haemophilus (15.0%)

     

Prevotella (11.4%)

     

Neisseria (5.0%)

     

Veillonella (2.9%)

023847

68.3%

23.8%

7.9%

0.954

Propionibacterium (61.5%)

(nose)

    

Staphylococcus (8.5%)

     

Achromobacter (7.5%)

     

Alteromonas (6.3%)

     

Desulfosporosinus (5.0%)

  1. Columns: (1) short read sample ID; (2) percentage of high confidence assignments; (3) percentage of low confidence assignments; (4) percentage of unassigned reads; (5) average confidence score for all assignments; (6) five most frequent genera in high confidence assignments (listed in decreasing order). An assignment is high confidence if the confidence score is higher than 0.75, low confidence otherwise.
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BMC Genomics

ISSN: 1471-2164

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