Table 1

Number of sequences assigned and unassigned in the MEGAN analysis.

Daphnia species/dataset

Assigned to cellular organisms

Assigned to Bacteria without Firmicutes1

Not assigned2

Sequences without hits


D. pulex

38,249

25,868

97,852

120,355

D. pulicaria

99,178

25,604

966,027

23,469

D. magna GS 20

3,028

2,560

16,007

26

D. magna GS FLX

4,781

4,285

21,535

12


1 The Firmicutes were excluded, because the D. magna datasets contained a bacterial parasite belonging into this taxon. For each dataset, the sum of columns 2, 4, and 5 is less than the total number of sequences analyzed (Table 2) due to the few sequences assigned to other NCBI taxonomy categories such as "Other" and "Unclassified".

2 The unassigned sequences are sequences without hits above the defined thresholds (See Materials and Methods). They may be A) sequences that do not have homologs in the current NCBI-nt database, B) sequences that evolved so strongly that their homologs are disguised by bit scores below our threshold or C) sequences that are assigned to species to which no other sequences is assigned (min-support threshold = 2).

Qi et al. BMC Genomics 2009 10:172   doi:10.1186/1471-2164-10-172

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