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Table 5 A Summary of characteristics of assemblies annotated without and with PacBio mRNA sequences

From: Improving eukaryotic genome annotation using single molecule mRNA sequencing

Statistic

Original A. ceylanicum genome annotation (AC-Orig)

Improved A. ceylanicum genome annotation using PacBio data (AC-PB)

AC-Orig genes overlapping (10%) AC-PB genes with PacBio evidence

AC-PB genes with PacBio evidence (with or without EST evidence)

Number of genes

16,026

17,540

6734

8238

Number of single exon genes

805

863

154

211

Total length of all exons (bp)

15,590,301

17,519,546

7,915,169

9,931,507

Total number of exons

117,877

121,578

63,273

67,714

Average exon length (bp)

132.3

144.1

125.1

146.7

Average # exons/gene

7.4

6.9

9.4

8.2

Total length of all CDS exons (bp)

15,429,981

15,685,322

28,877,304

27,490,435

Total number of CDS exons

117,657

119,866

63,129

66,083

Average CDS exon length (bp)

131.1

130.9

123.5

123.2

Average # coding exons/gene

7.3

6.8

9.4

8.0

Total length of all introns (bp)

63,133,642

60,868,345

28,930,431

28,142,643

Total number of introns

101,851

104,038

56,566

59,476

Average intron length (bp)

621.2

594.9

511.7

473.2

Average # introns/gene

6.4

5.9

8.4

7.2

Total UTR length (bp)

160,320

1,834,224

117,930

1,788,957

Number of genes with UTR

1889

7295

1205

6567

Average size of UTR per gene with UTR

84.9

251.4

97.9

272.4

Number of genes with UTR < 10 bp

1228

3966

744

3451

Number of genes with UTR 10 bp - 100 bp

423

1058

287

908

Number of genes with UTR > 100 bp

238

2271

174

2208

Total 5’ UTR length (bp)

63,556

300,333

39,954

273,401

Number of genes with 5’ UTR

1150

3488

710

3013

Number of genes with spliced 5’ UTR

127

745

82

696

Total 3’ UTR length (bp)

96,764

1533,891

77,976

1515,556

Number of genes with 3’ UTR

1238

6611

817

6145

Number of genes with spliced 3’ UTR

45

400

33

388

# of ESTs at 3’

–

–

3610

105,053

polyA signal ‘aataaa/attaaa’

–

–

1307

61,069

polyA signal ‘agtaaa’ only

–

–

215

7775

polyA total (any signal)

–

–

1522

68,844