Codon adaptation index above 1 when all genes are used as reference

[CongLiu37]

Hello,

I am computing codon usage index for all genes in a genome and I use all genes as reference:

>cds=readSet(file="cds.fna")
>codon.table=codonTable(cds)
>head(codon.table)
codonTable instance with codon counts from 6 sequences.
               ID length AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA
1 Aaca00009242-R0    701  25  11  12  26  15   6  13  12   9   2   4  14  29
2 Aaca00009243-R0    375   0   0   0   1   0   0   0   0   0   0   0   8   3
3 Aaca00009244-R0    782  17  18  20  16  21   8  11  18  16   8   9  11  16
4 Aaca00009245-R0    797   8  20  20  17  11  14  14  15   9  11   9  14  15
5 Aaca00009246-R0   1010  26  21  10  16  22  14  12  21  13  17   7  15  19
6 Aaca00009247-R0    709  17  13  11  17  21  12   6  13   9   9   8  13  13
  ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT
1   7  13  27  16   9  10  12   9   3   7   9   4   2   1   6  11  11  10  14
2   0   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0
3  16  15  22   7  16  15   4   9   8   2   5   8   4   5   6   6   8  32  15
4  17  16  14  12  15  20   8   7   5   3  11   7   9   3   7  10  14  32  15
5  21  24  15  25   9  24  11  17   8  11  17   8   5   3  10  15  19  31  21
6   8  17  18  12  10  12  11  11   1   6   8   2   3   2   5  10  15  32  12
  GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG
1  28  12   8  22   7   5   7   8  10   2   2   7  19   5   9  22   0  12   1
2   0   0   0   9   0   0   0   1   0   3   0 330   0   0   3   4   0   0   0
3  13  23  10  15  11  11   8  20  10  16   7   6  11   8  19  16   1  24   0
4  17  17  10  12  16  15  12  22  11  13   3  12   9  16  31  15   0  20   0
5  34  18  13  25  10  12   8  21  18  14  11  22  14  17  13  15   1  27   0
6  20  13   5  13  18   9   2  15  20   9   5  10   8  15  16  11   1  14   0
  TAT TCA TCC TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT
1  21  15  10   4  12   0   4  14   7  14  30   7  18
2   4   0   0   0   0   1   0   0   3   0   0   1   2
3  11   8  11  11  11   0   9  16  14   8  19  22  21
4  13  12  11   6   8   1  13  15   8   8  21  12  16
5  13  18  17  16  28   0  10  19   7  10  23  29  20
6  12   8   4  11   9   0   9  20   9  12  16  19  19
>cai=CAI(cTobject=codon.table,subsets=list(codon.table))

In the 16,706 genes, 3,887 have codon adaptation index above 1. I assume it is not related with #14 or #2, as I have all genes as reference.

Sincerely,

Cong