Abbreviations

The abbreviations used are:

Coordinates Coordinates of the gene

Strand Strand

Length Length of the sequence in bp

PID Number code of the gene

Gene name Gene name

Synonym Synonym gene name

FunctionCode Functional classification of the gene according with the Cluster of Ortologous Genes (COG) database

COG COG family that the gene belong

GCRegion "-" indicates that the gene belong to a region with a low G+C content; "+" indicates that the gene belong to a region with a high G+C content.
"f" indicates that the gene has been filtered and it is not predicted as being acquired or not acquired

HGT "H" indicates a potential horizontally transferred gene and "f" indicates that the gene has been filtered and it is not predicted as being acquired or not acquired

Function Function of the gene

GC1 G+C content of first codon position

SD1 Number of Standard Deviations (SD) from G+C1 mean

Sim1 "1" indicates deviations more than 1.5 SD and "2" more than 2 SD. "+" indicates positive deviations; and "-" negative deviations

GC2 G+C content of second codon position

SD2 Number of Standard Deviations (SD) from G+C2 mean

Sim2 "1" indicates deviations more than 1.5 SD and "2" more than 2 SD. "+" indicates positive deviations; and "-" negative deviations

GC3 G+C content of third codon position.

SD3 Number of Standard Deviations (SD) from G+C3 mean

Sim3 "1" indicates deviations more than 1.5 SD and "2" more than 2 SD. "+" indicates positive deviations; and "-" negative deviations

GCT Total G+C content.

SDT Number of Standard Deviations (SD) from G+CT mean

SimT "1" indicates deviations more than 1.5 SD and "2" more than 2 SD. "+" indicates positive deviations; and "-" negative deviations

SimGC "1" indicates potential "odd" gene in the G+C content; "2" indicates "odd" gene in the G+C content.

Mah Mahalanobis distance of the gene.

SimMah "1" indicates potencial "odd" gene in the codon usage; "2" indicates "odd" gene in the codon usage

Dev.AA Amino acids whose content deviates more than 3SD from the mean content and number of SD

Others abbreviations used in the correspondence analysis of relative synonymous codon usage are:

Nc Effective number of codons (Wright 1990. Gene 87, 23-29). Gives the number of equally used codons which would generate the same codon usage bias as observed. A gene utilizing only one codon per amino acid has the strongest bias and the minimum index value (20). A gene using all codons equally has a value of 61.

P2 Translational efficiency (Gouy and Gautier 1982. NAR 10, 7055-7074). Describes the proportion of codons conforming to the intermediate strength of codon-anticodon interaction energy rule of Grosjean and Fiers. It goes between 0 i 1.

ICDI Intrinsec codon bias index (ICDI) (Freire-Picos et al. 1994. Gene 139, 43-49). Range between 0 for non biassed and 1 for biassed genes.

Chi² Scaled Chi²(Shileds and Sharp 1987. NAR 15, 8023-8040). This index messures the degree of bias due to a non uniformous use of synomous codons of a gene, using uniform synonymous codon usage as the expectation.

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Coordinates	Coordinates of the gene
Strand	Strand
Length	Length of the sequence in bp
PID	Number code of the gene
Gene name	Gene name
Synonym	Synonym gene name
FunctionCode	Functional classification of the gene according with the Cluster of Ortologous Genes (COG) database
COG	COG family that the gene belong
GCRegion	"-" indicates that the gene belong to a region with a low G+C content; "+" indicates that the gene belong to a region with a high G+C content. "f" indicates that the gene has been filtered and it is not predicted as being acquired or not acquired
HGT	"H" indicates a potential horizontally transferred gene and "f" indicates that the gene has been filtered and it is not predicted as being acquired or not acquired
Function	Function of the gene
GC1	G+C content of first codon position
SD1	Number of Standard Deviations (SD) from G+C1 mean
Sim1	"1" indicates deviations more than 1.5 SD and "2" more than 2 SD. "+" indicates positive deviations; and "-" negative deviations
GC2	G+C content of second codon position
SD2	Number of Standard Deviations (SD) from G+C2 mean
Sim2	"1" indicates deviations more than 1.5 SD and "2" more than 2 SD. "+" indicates positive deviations; and "-" negative deviations
GC3	G+C content of third codon position.
SD3	Number of Standard Deviations (SD) from G+C3 mean
Sim3	"1" indicates deviations more than 1.5 SD and "2" more than 2 SD. "+" indicates positive deviations; and "-" negative deviations
GCT	Total G+C content.
SDT	Number of Standard Deviations (SD) from G+CT mean
SimT	"1" indicates deviations more than 1.5 SD and "2" more than 2 SD. "+" indicates positive deviations; and "-" negative deviations
SimGC	"1" indicates potential "odd" gene in the G+C content; "2" indicates "odd" gene in the G+C content.
Mah	Mahalanobis distance of the gene.
SimMah	"1" indicates potencial "odd" gene in the codon usage; "2" indicates "odd" gene in the codon usage
Dev.AA	Amino acids whose content deviates more than 3SD from the mean content and number of SD

Nc	Effective number of codons (Wright 1990. Gene 87, 23-29). Gives the number of equally used codons which would generate the same codon usage bias as observed. A gene utilizing only one codon per amino acid has the strongest bias and the minimum index value (20). A gene using all codons equally has a value of 61.
P2	Translational efficiency (Gouy and Gautier 1982. NAR 10, 7055-7074). Describes the proportion of codons conforming to the intermediate strength of codon-anticodon interaction energy rule of Grosjean and Fiers. It goes between 0 i 1.
ICDI	Intrinsec codon bias index (ICDI) (Freire-Picos et al. 1994. Gene 139, 43-49). Range between 0 for non biassed and 1 for biassed genes.
Chi²	Scaled Chi²(Shileds and Sharp 1987. NAR 15, 8023-8040). This index messures the degree of bias due to a non uniformous use of synomous codons of a gene, using uniform synonymous codon usage as the expectation.