Analysis of intra-genomic GC content homogeneity within prokaryotes

BMC Genomics

Table 1 The coefficient estimates from the GCVAR regression model

Factor	Category	Chromosomes	Average %GC	Average size (mbp)	Coefficient estimate	p-value
Phylum	Acidobacteria	2	60	7.8	-0.23	0.05
Phylum	Actinobacteria	42	66	4.8	-0.11	0.003
Phylum	Bacteroides	16	44	3.6	0.18	<0.001
Phylum	Betaproteobacteria	64	64	3.4	0.1	0.002
Phylum	Chlamydiae	8	43	1.9	-0.28	<0.001
Phylum	Crenarchaeota	16	48	2	0.22	<0.001
Phylum	Cyanobacteria	17	48	4.4	0.3	<0.001
Phylum	Deltaproteobacteria	18	58	4.7	0.15	0.001
Phylum	Epsilonproteobacteria	12	38	1.9	0.1	0.04
Phylum	Euryarcheota	31	46	2.4	0.16	<0.001
Phylum	Firmicutes	89	37	2.6	0.12	<0.001
Phylum	Gammaproteobacteria	92	47	3.7	0.12	<0.001
Phylum	Planctomycetes	1	55	7.2	-0.48	0.002
Phylum	Spirochaetes	11	37	1.7	0.14	0.01
Oxygen	Anaerobic	-	-	-	0.11	<0.001
GC	-	-	-	-	0.37	<0.001

The variable GC is continuous while phylum and oxygen are categorical variables. Note that for the phylum variable we have used the sum-to-zero parameterization, i.e. all estimated effects are deviations from the mean phylum effect. For the oxygen requirement variable however, we used a relative parameterization where the category "aerobic" is the reference, i.e. the estimated effect is the deviation from the aerobic effect. In addition, the number of chromosomes, average %GC, and average genomes size in mbp, are included for each phylogenetic group.

ISSN: 1471-2164