Skip to main content
. 2014 Feb 28;197(1):301–315. doi: 10.1534/genetics.114.162842

Table 3. Results of fitting the linear regression model in Equation 3 to codon usage in dsDNA E. coli phages, with viral genome accession number (ACCN), the estimated intercept (BC→T) and slope (b), the Pearson correlation between PU and φ for each phage species, and the statistical significance (two-tailed P) of the relationship.

Phage ACCN BC→T b R Pa
Phage 13a NC_011045 0.5690 1.3782 0.8381 0.00005b
Phage 285P NC_015249 0.5769 1.4737 0.8751 0.00001b
Phage 933W NC_000924 0.5543 0.0089 0.0129 0.96205
Phage BP-4795 NC_004813 0.5210 −0.2133 −0.2768 0.29931
Phage CC31 NC_014662 0.7277 1.0780 0.8437 0.00004b
Phage cdtI NC_009514 0.5632 −0.2310 −0.2948 0.26777
Phage EcoDS1 NC_011042 0.5477 1.4925 0.8077 0.00015b
Phage EPS7 NC_010583 0.7368 0.8949 0.9011 0.00000b
Phage HK022 NC_002166 0.4858 0.1603 0.1659 0.53920
Phage HK97 NC_002167 0.4951 0.2864 0.2699 0.31203
Phage IME08 NC_014260 0.7156 0.6011 0.6583 0.00557c
Phage JK06 NC_007291 0.6157 0.7818 0.5302 0.03462
Phage JS10 NC_012741 0.7206 0.6104 0.6538 0.00601c
Phage JS98 NC_010105 0.7200 0.6300 0.6684 0.00464c
Phage JSE NC_012740 0.6931 0.6136 0.5988 0.01425c
Phage K1-5 NC_008152 0.6612 0.9844 0.8118 0.00013b
Phage K1E NC_007637 0.6605 0.9377 0.8209 0.00010b
Phage K1F NC_007456 0.6605 0.9377 0.8209 0.00010b
Phage lambda NC_001416 0.4971 −0.1962 −0.1908 0.47894
Phage Min27 NC_010237 0.5504 0.0858 0.1302 0.63088
Phage Mu NC_000929 0.4980 −0.6273 −0.5245 0.03700
Phage N15 NC_001901 0.4834 0.0208 0.0231 0.93224
Phage N4 NC_008720 0.7556 0.9110 0.8554 0.00002b
Phage P1 NC_005856 0.5475 0.0698 0.0885 0.74454
Phage P2 NC_001895 0.4768 −0.4703 −0.4765 0.06202
Phage P4 NC_001609 0.5065 −0.6610 −0.5315 0.03412
Phage Phi1 NC_009821 0.6905 0.5815 0.5728 0.02039c
Phage Phieco32 NC_010324 0.7277 1.1889 0.9436 0.00000b
Phage phiEcoM-GJ1 NC_010106 0.6421 1.0372 0.8690 0.00001b
Phage phiP27 NC_003356 0.5451 −0.3341 −0.3569 0.17473
Phage PRD1 NC_001421 0.5324 −0.5638 −0.2643 0.32262
Phage RB16 NC_014467 0.6257 1.0301 0.7718 0.00046b
Phage RB49 NC_005066 0.6919 0.5836 0.5790 0.01878c
Phage RB69 NC_004928 0.7549 0.6396 0.7414 0.00101b
Phage RTP NC_007603 0.6092 0.8781 0.5433 0.02964
Phage SfV NC_003444 0.5316 −0.1209 −0.1431 0.59705
Phage SPC35 NC_015269 0.7544 0.6200 0.8677 0.00001b
Phage SSL-2009a NC_012223 0.3735 0.2555 0.3003 0.25843
Phage T1 NC_005833 0.5786 0.9154 0.5723 0.02053c
Phage T3 NC_003298 0.5336 1.3661 0.8663 0.00001b
Phage T4 NC_000866 0.7967 0.3770 0.5538 0.02603
Phage T5 NC_005859 0.7386 0.5950 0.8399 0.00005b
Phage T7 NC_001604 0.5641 1.3971 0.8461 0.00004b
Phage TLS NC_009540 0.6377 0.5840 0.3261 0.21766
Phage vB_EcoM-VR7 NC_014792 0.6945 0.4866 0.6418 0.00736c
Phage VT2-Sakai NC_000902 0.5434 0.0377 0.0517 0.84906
Phage WV8 NC_012749 0.7372 1.0841 0.9077 0.00000b
Phage bV_EcoS_AKFV3 NC_017969 0.7444 0.5894 0.8094 0.00015b
Phage D108 NC_013594 0.4994 −0.5957 −0.4791 0.06045
Phage HK639 NC_016158 0.4491 0.2538 0.2437 0.36316
Phage HK75 NC_016160 0.4839 0.3029 0.3018 0.25602
Phage phiV10 NC_007804 0.5705 0.4618 0.4478 0.08199
Phage rv5 NC_011041 0.6296 0.8548 0.6931 0.00291b
Phage vB_EcoM_CBA12 NC_016570 0.5988 0.3685 0.4449 0.08425
Stx1-converting bac NC_004913 0.5512 0.0121 0.0165 0.95162
Phage BA14 NC_011040 0.5691 1.4057 0.8765 0.00001b
Stx2-converting phage II NC_004914 0.5479 0.0495 0.0706 0.79503
Stx2-converting phage 1717 NC_011357 0.5011 −0.1374 −0.1724 0.52309
Stx2-converting phage 86 NC_008464 0.5681 0.0285 0.0417 0.87813
Stx2-converting phage I NC_003525 0.5132 −0.0566 −0.0986 0.71646
a

Significant at the 0.05 level when experimentwise error rate is controlled by the false discovery rate method.

b

Significant with the more conservative approach of Benjamini and Yekutieli (2001).

c

Significant with the approach of Benjamini and Hochberg (1995).