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I was wondering if anybody knows how many reads from metagenomic or metatranscriptomic data do not map to known sequences and are therefore unidentifiable?

I found a figure for viromics, which seems to indicate that only about 6% of the sequences correspond to known virus (http://www.pnas.org/content/111/29/10714.full). But I couldn't find a more general percentage.

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I think this will vary greatly depending on the source environment. Your example (marine viruses) is probably due to the large diversity of ocean viruses of which most have no reference genome.

Referencing the Human Microbiome Project:

A total of 57.6% of the high-quality microbial reads could be associated with a 
known genome (ranging from 33–77% for anterior nares and posterior fornix, respectively).

Other papers describing more recent k-mer based approaches for classification report between 40-90% classified to a known reference. See:

http://www.nature.com/articles/srep19233

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4401624/

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