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Table 2 Percentage of dinucleotide at the starting position of all mapped reads.

From: Bias detection and correction in RNA-Sequencing data

  

Mamanova et al.

Marioni et al.

Bullard et al.

Lee et al

Nagalakshmi et al.

Dinuc

Read type

STD-Seq

FRT- Seq

Marioni kidney

Marioni liver

MAQC2 brain

MAQC2 UHR

MAQC3 UHR

yeast RH

yeast oligodT

yeast RH

AA

unique

4.5

9.3

6.1

8.4

2.1

2.2

2.7

5.2

10.8

10.3

AA

multi

4.5

10.3

6.7

7.9

2.5

2.6

3.0

4.0

10.1

7.9

AC

unique

1.5

5.2

1.4

1.4

0.9

1.0

0.8

1.4

6.4

5.4

AC

multi

2.1

5.8

1.3

1.3

1.0

1.0

0.9

1.3

6.0

5.2

AG

unique

2.5

7.1

3.0

3.2

2.2

2.2

2.2

2.3

7.8

5.9

AG

multi

3.3

6.6

2.8

3.0

2.1

2.2

2.1

2.0

6.9

4.8

AT

unique

3.4

7.2

5.7

6.8

1.9

2.0

2.4

4.7

7.4

5.7

AT

multi

3.9

5.4

6.0

7.0

2.3

2.4

2.7

4.3

7.8

5.0

CA

unique

8.9

5.4

7.7

7.0

10.7

10.6

10.5

8.7

10.6

11.1

CA

multi

7.3

5.2

6.2

5.6

10.0

11.0

10.9

7.8

10.9

10.2

CC

unique

9.6

4.0

7.8

5.8

10.8

10.2

10.4

5.6

6.0

6.3

CC

multi

9.0

4.2

7.2

5.4

9.6

8.8

9.4

7.3

5.5

7.7

CG

unique

5.5

2.3

4.4

3.4

10.0

10.1

10.4

7.2

2.0

2.9

CG

multi

5.8

2.9

5.2

4.6

9.9

8.7

9.1

8.6

2.2

4.3

CT

unique

12.2

5.8

13.3

11.6

13.1

13.0

13.3

12.2

7.9

7.4

CT

multi

13.0

6.0

13.0

11.2

13.4

13.5

13.7

13.1

7.8

9.1

GA

unique

4.0

6.7

4.9

5.3

5.2

5.4

4.5

7.0

4.9

5.4

GA

multi

4.5

6.1

4.7

5.2

5.3

5.8

4.7

6.2

5.0

5.3

GC

unique

12.5

5.7

7.7

6.9

11.7

12.0

10.0

8.6

2.2

3.0

GC

multi

11.2

6.2

8.1

7.6

11.1

11.6

9.8

10.3

1.8

3.2

GG

unique

13.0

5.0

9.2

8.8

12.0

11.9

11.8

8.7

3.8

4.2

GG

multi

11.7

6.0

9.8

9.6

11.7

11.4

11.1

8.6

4.1

5.2

GT

unique

9.8

5.7

10.1

9.5

8.4

8.6

8.4

12.3

4.2

5.2

GT

multi

9.2

5.0

10.4

10.0

9.2

9.1

9.1

11.8

4.6

6.9

TA

unique

1.6

5.2

3.7

4.4

1.1

1.1

1.3

2.2

10.8

10.8

TA

multi

1.7

3.8

4.3

5.0

1.4

1.1

1.4

2.1

11.2

10.3

TC

unique

2.1

6.8

3.0

3.2

2.1

2.2

2.3

2.9

3.9

4.8

TC

multi

2.8

6.0

2.7

3.0

2.1

2.2

2.3

3.0

3.8

4.2

TG

unique

6.1

6.9

5.6

5.6

4.7

4.9

5.4

5.1

7.9

8.4

TG

multi

5.7

8.2

5.5

5.6

4.8

5.3

5.8

4.7

8.7

7.8

TT

unique

2.7

11.4

6.3

8.4

2.5

2.5

3.6

5.9

3.5

3.3

TT

multi

4.1

12.1

6.2

7.9

2.9

2.9

4.0

4.8

3.4

2.7

  1. Percentage was calculated by SAMStat [33]. Uniquely mapped reads and multi-mapped reads were separated in the calculation but showed similar pattern. Bold numbers indicates significantly over-represented dinucleotide with p-values less than or equal to 10-100 from a Binomial test described in [34].