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Table 3 Responses of GC1 and GC2 to changes in GC3, by domain

From: A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes

 

n

 

R 2

Slope ± SE

Y at GC3 = 0 ± SE

Y at GC3 = 100 ± SE

Bacteria

311

GC1

0.91

0.370 ± 0.007

0.367 ± 0.004

0.737 ± 0.003

  

GC2

0.80

0.219 ± 0.006

0.291 ± 0.004

0.510 ± 0.003

Archaea

28

GC1

0.85

0.38 ± 0.03

0.35 ± 0.02

0.73 ± 0.02

  

GC2

0.60

0.16 ± 0.03

0.30 ± 0.01

0.45 ± 0.01

Eukaryotes

257

GC1

0.57

0.24 ± 0.01

0.402 ± 0.008

0.643 ± 0.007

  

GC2

0.38

0.15 ± 0.01

0.334 ± 0.007

0.482 ± 0.006

  1. Because there is error in both axes, but there should be a definite causal relationship between GC3 and GC1 or GC2, we use model I regression to predict specific values of GC1 or GC2 from a set value of GC3, and thus to calculate the most likely proportion and GC content of constant sites [73].
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Genome Biology

ISSN: 1474-760X

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