Table 1. Codon frequencies (CF) for Y-ending codons in E. coli, compiled for highly expressed genes (HEG) and all other genes (non-HEG), together with the gene copy number of tRNA in the genome (strain K12) whose anticodon matches the codon, and φ as a measure of codon preference of the host translation machinery (a large φ corresponds to greater preference of U-ending codons over C-ending codons).

AA	Codon	CFnon-HEG	CFHEG	tRNA	φ
A	GCC	33,463	1,306	2	0.1424
A	GCT	18,526	2,288
C	TGC	8,397	475	1	−0.0362
C	TGT	6,802	270
D	GAC	23,226	2,786	3	−0.0993
D	GAT	41,472	2,345
F	TTC	20,332	2,229	2	−0.1478
F	TTT	29,556	872
G	GGC	37,418	2,987	4	0.0566
G	GGT	30,154	3,583
H	CAC	12,144	1,160	1	−0.1331
H	CAT	17,170	477
I	ATC	30,787	3,488	3	−0.1232
I	ATT	39,788	1,640
L	CTC	14,591	541	1	−0.0353
L	CTT	14,679	357
N	AAC	26,674	2,832	4	−0.1512
N	AAT	23,652	539
P	CCC	7,443	38	1	0.1032
P	CCT	9,235	343
R	CGC	28,473	1,530		0.1011
R	CGT	25,528	2,995	3a
S	AGC	20,868	1,015	1	−0.0842
S	AGT	11,802	168
S	TCC	10,649	1,110	2	0.0327
S	TCT	10,217	1,320
T	ACC	29,335	2,533	2	0.0408
T	ACT	10,950	1,286
V	GTC	19,972	824	2	0.1262
V	GTT	22,297	2,669
Y	TAC	15,094	1,569	3	−0.1122
Y	TAT	21,207	865

P-values from a chi-square test of 2 × 2 contingency tables, with the null hypothesis that φ = 0, are all <0.0001.

^aThe anticodon has a wobble A modified to inosine.