Table 1.

Sequence variation in VPI genes of N16961 (seventh pandemic) and 395 (sixth pandemic)

Gene or intergenic regionaLength (bp)No. of:% DifferenceKsKaKs/Karatio
Polymorphic sitesNonsynonymous sites
orf1 978200.2040.0055900
aldA 1,521000000
tagA 3,009530.1660.003060.001771.72881
Intergenic1
orf2 1,1161000.000990
orf3 2,8892490.8310.015830.004663.39699
orf4 9392252.3430.06690.009097.35973
Intergenic7
tagD 495621.2120.024230.006193.91437
Intergenic21
tcpI 1,863830.4290.008490.002283.72368
Intergenic45
tcpP 6661051.5020.017470.012121.44141
tcpH 4111152.6760.106260.016146.58364
Intergenic67
tcpA 6751524522.5191.05880.121878.68852
Intergenic25
tcpB 1,2931931.4690.046010.0033213.8584
tcpQ 453921.9870.087090.0083710.4050
tcpC 1,4703232.1770.091580.0036824.8858
tcpR 45600000
tcpD 82200000
tcpS 459110.21800.003390
tcpT 1,512110.06600.000760
tcpE 1,02300000
tcpF 1,017330.29500.004560
Intergenic1
toxT 83100000
tcpJ 762200.2620.0073000
acfB 1,881220.10600.001640
acfC 76200000
orfY 47400000
tagE 90900000
acfA 64800000
acfD 4,563000000
Intergenic1
int 1,26900000
  • a ∗, for orf2, orf3, andacfD, the largest common segment was used. See the text for details. The frameshift mutation was not included as a polymorphic site for this purpose.