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Table 5 Violations of the 2nd Chargaff rule on HG38. Columns contain the values of #T/#A, #G/#C on different chromosomes, as well as their Y and Z values. The latter reflect the significance of the inequality

From: Inversion symmetry of DNA k-mer counts: validity and deviations

 

T/A

G/C

Y(T,A)

Y(G,C)

Z(T,A)

Z(G,C)

chr1

1.002593

1.001175

0.001295

0.000587

15

5.76

chr2

1.00274

1.002747

0.001368

0.001372

16.41

13.49

chr3

1.002416

1.002824

0.001207

0.00141

13.19

12.5

chr4

1.001062

1.002595

0.000531

0.001296

5.75

11.04

chr5

1.004679

1.004144

0.002334

0.002068

24.44

17.5

chr6

1.000537

1.001981

0.000268

0.000989

2.72

8.12

chr7

1.003332

1.001884

0.001663

0.000941

16.15

7.57

chr8

0.999241

1.002536

−0.00038

0.001266

−3.53

9.65

chr9

1.001327

1.002823

0.000663

0.001409

5.61

9.99

chr10

1.0039

1.002911

0.001946

0.001454

17.18

10.82

chr11

1.001915

1.002815

0.000956

0.001405

8.48

10.51

chr12

1.003102

1.003317

0.001548

0.001656

13.75

12.2

chr13

1.003831

1.005012

0.001912

0.002499

14.83

15.36

chr14

1.008943

1.007342

0.004451

0.003658

32.58

22.24

chr15

1.001842

1.00411

0.00092

0.002051

6.44

12.23

chr16

1.009601

1.007001

0.004778

0.003488

32.17

21.07

chr17

1.002905

1.006812

0.00145

0.003395

9.77

20.81

chr18

1.005494

1.016917

0.00274

0.008388

19.03

47.34

chr19

1.009276

1.007636

0.004617

0.003803

25.46

20.13

chr20

1.011147

1.012815

0.005542

0.006367

33.22

33.7

chr21

1.003017

1.005026

0.001506

0.002507

7.33

10.15

chr22

0.998893

1.009337

−0.00055

0.004647

−2.52

19.94

chrX

1.003463

1.005699

0.001728

0.002842

16.73

22.23

chrY

1.008873

1.000209

0.004417

0.000105

17.58

0.34

  1. All Z values are very significant, but for Z(G,C) on chrY which corresponds to a p-value of 0.367. All other have inequality p-values < 0.01. On all chromosomes we observe #G > #C on the positive strand. Same is true for #T > #A, but for chr8 and chr22, where #T < #A, which is also a significant observation (|Z| > 2.575 corresponds to an inequality p-value < 0.005)