Table 7

GC percentages (averaged over all reads) in open reading frames identified using Metagene

DNA reads

RNA reads


Site

Depth (m)

Alla

DNA onlyb

DNA+RNAc

Alla


OMZ

50

37.6

38.2

36.0

42.8

85

38.2

38.4

36.7

44.9

110

41.1

42.6

38.1

42.8

200

40.9

41.9

38.6

45.6

BATS 216

20

34.5

35.4

33.8

42.8

50

35.2

36.4

33.9

40.3

100

33.7

34.7

32.9

37.8

HOT 186

25

35.5

36.0

34.8

44.0

75

34.9

35.2

34.4

41.4

110

36.0

36.4

35.0

40.0

500

43.2

43.1

43.5

50.6

Soil

Surface

62.7

63.1

62.5

62.6


aAll reads identified as 'protein-coding' via significant BLASTX matches to NCBI-nr (bit-score > 50), with GC content then estimated for Metagene-called open reading frames within this read set. bReads matching genes detected only in the DNA data. cReads matching genes detected in both the DNA and RNA data. BATS, Bermuda Atlantic Time Series; BLAST, Basic Local Alignment Search Tool; GC, guanine-cytosine; HOT, Hawaii Ocean Time Series; HSP, high-scoring segment pair; NCBI-nr, National Center for Biotechnology Information non-redundant protein database; OMZ, oxygen minimum zone.

Stewart et al. Genome Biology 2011 12:R26   doi:10.1186/gb-2011-12-3-r26

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