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Table 3 Illumina and Pacbio RNA-Seq read coverage over predicted gene sets

From: Improving eukaryotic genome annotation using single molecule mRNA sequencing

Read Type

Gene Set

Subset of genes

Total count

# of expressed genes (breadth ≥50%)

% expressed

Average read depth

Any

Expressed

Illumina Reads

AC-Orig

All genes

16,026

10,405

64.9%

161.1

245.6

Overlapping AC-PB genes

15,808

10,254

64.9%

160.9

245.5

Not overlapping AC-PB genes

218

151

69.3%

171.3

246.4

AC-PB

All genes

17,540

11,721

66.8%

156.3

231.6

Overlapping AC-Orig genes

15,931

10,365

65.1%

158.3

240.8

Not overlapping AC-Orig genes

1609

1356

84.3%

136.5

161.1

Schwarz et al., [31]

36,687

16,376

44.6%

90.4

199.4

PacBio Reads

AC-Orig

All genes

16,026

3166

19.8%

3.3

8.9

Overlapping AC-PB genes

15,808

3128

19.8%

3.2

8.8

Not overlapping AC-PB genes

218

38

17.4%

4.1

12.8

AC-PB

All genes

17,540

4209

24.0%

3.6

8.8

Overlapping AC-Orig genes

15,931

3398

21.3%

3.4

8.7

Not overlapping AC-Orig genes

1609

811

50.4%

6.4

9.1

Schwarz et al., [31]

36,687

4903

13.4%

2.1

8.8