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Table 1 Local and global PS of bacterial chromosomes

From: Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns

Bacterial chromosome

Length (bp) of sequence

Global n0_4mer PS (%)

Local n0_4mer PS (%)*

 

Total

Coding

Non-coding

Total

Coding

Non-coding

Median (inner quartiles, range)

Aeropyrum pernix K1

1,669,695

1,490,824

178,871

4.92

4.46

7.81

9.61 (6.19 – 13.63, 4.37 – 41.24)

Aquifex aeolicus VF5

1,551,335

1,448,950

102,385

3.40

3.49

8.18

5.37 (4.15 – 7.36, 2.89 – 32.50)

Bacillus subtilis 168

4,214,814

3,684,952

529,862

2.50

2.40

5.27

23.71 (21.50 – 26.81, 4.36 – 47.16)

Bradyrhizobium japonicum USDA 110

8,619,960

7,515,107

1,104,853

1.27

1.38

3.01

5.89 (5.18 – 7.09, 2.18 – 23.18)

Campylobacter jejuni NCTC 11168

1,641,481

1,555,799

85,682

2.26

2.49

15.10

15.86 (11.46 – 20.79, 1.80 – 28.85)

Corynebacterium glutamicum ATCC 13032

3,309,401

2,867,342

442,059

3.71

3.49

9.68

17.84 (16.45 – 21.99, 6.26 – 56.73)

Escherichia coli K-12

4,639,221

4,096,745

542,476

2.15

2.44

5.85

15.01 (12.04 – 23.11, 2.86 – 49.02)

Mycoplasma pulmonis UAB CTIP

963,879

869,493

94,386

2.45

2.52

6.37

Not applicable

Prochlorococcus marinus MIT9313

2,410,873

1,982,808

428,065

15.97

15.75

14.45

31.40 (19.54 – 35.60, 3.46 – 45.97)

Prochlorococcus marinus ssp. marinus CCMP1375

1,751,080

1,566,066

185,014

1.82

1.81

4.85

9.99 (6.89 – 12.90, 1.58 – 37.52)

Pseudomonas putida KT2440

6,181,863

5,439,657

742,206

2.75

2.22

5.85

10.95 (9.67 – 12.91, 2.14 – 22.30)

Rhodopirellula baltica 1

7,145,576

6,817,640

327,936

3.45

3.45

6.65

14.83 (11.77 – 17.05, 3.69 – 26.42)

Staphylococcus aureus N315

2,814,816

2,357,692

457,124

2.12

2.04

3.78

22.21 (19.99 – 23.74, 7.27 – 38.55)

Streptomyces coelicolor A3(2)

8,667,507

7,379,401

1,288,106

1.48

1.42

1.77

4.70 (3.51 – 6.52, 1.91 – 20.42)

Xylella fastidiosa 9a5c

2,679,306

2,244,990

434,316

24,27

21.00

36.74

50.64 (39.86 – 57.52, 7.41 – 68.29)

Xylella fastidiosa Temecula1

2,519,802

1,967,507

552,295

6.38

5.02

13.69

53.17 (41.73 – 59.23, 8.80 – 71.71)

  1. *PS values of n0_4mer patterns were calculated for 100 arbitrary loci (200 for E. coli and B. subtilis) of 5 to 1,000 kbp in size (median 289,752 bp, inner quartiles 114,406 – 477,801 bp).
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BMC Bioinformatics

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