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Table 5 Numbers and percentages of Douglas-fir sequences with matches to sequences in the Uniref50 protein database*

From: A SNP resource for Douglas-fir: de novotranscriptome assembly and SNP detection and validation

 

Isogroups (25,002)†

Singletons (102,623)§

 

Isogroups with 1 isotig (I1 = 18,774)

Isogroups with >1 isotig (IM = 6228)

Singletons (S = 102,623)

Taxonomic category

Number

Percent of matches

Number

Percent of matches

Number

Percent of matches

Conifers

4088

27.16

1073

31.14

6486

25.18

Other plants

9713

64.52

2047

59.40

16,061

62.36

Other Eukaryotes

582

3.87

182

5.28

658

2.55

Invertebrates

487

3.24

120

3.48

1087

4.22

Bacteria

123

0.82

8

0.23

830

3.22

Environmental

21

0.14

6

0.17

37

0.14

Vertebrates

17

0.11

6

0.17

92

0.36

Fungi

19

0.13

4

0.12

487

1.89

Viruses

4

0.03

0

0.00

19

0.07

Total matches

15,054

100.00

3446

100.00

25,757

100.00

Unmatched

3720

-

2782

-

76,866

-

Percent matched

80.2

-

55.3

-

25.1

-

  1. *Matches are grouped by taxonomic affiliation and percentages are relative to the total number of matches (tBLASTX E-value < 10-5). Numbers of input Douglas-fir sequences are in parentheses.
  2. †Isogroups are Newbler v2.3 isogroups. For the isogroups with more than 1 isotig (IM subset), a hit was counted only if all isotigs matched the same protein in the database.
  3. §Singletons are 454 reads that did not assemble with any other reads.
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BMC Genomics

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