Table 3.

Polymorphism observed in the each epitope sequence

Epitope name	Epitopa	Segregating sites (S)	Singleto n variable sites	Parsimony informative sites	Total no. of mutations	K	H	Hd ± SD	π ± SD	Kn	Ks	Tajima's D
5	T/B	3	0	3	3	0.565	4	0.383 ± 0.079	0.013 ± 0.003	0.016	0	-0.289 (P > 0.1)
13	T	0	0	0	0	0	1	0	0	0	0	0
16	T/B	1	0	1	1	0.509	2	0.509 ± 0.013	0.011 ± 0.000	0.015	0	1.741 (P > 0.05)
18	B	1	0	1	1	0.509	2	0.509 ± 0.013	0.011 ± 0.000	0.015	0	1.741 (P > 0.05)
20	T/B	1	0	1	1	0.509	2	0.509 ± 0.013	0.011 ± 0.000	0.014	0	1.741 (P > 0.05)
28	None	0	0	0	0	0	1	0	0	0	0	0
40	None	3	0	3	3	0.867	3	0.542 ± 0.059	0.019 ± 0.003	0.018	0.025	0.642 (P > 0.1)
48	B	5	0	5	5	1.560	6	0.748 ± 0.040	0.035 ± 0.003	0.041	0	1.007 (P > 0.1)
54	None	0	0	0	0	0	1	0	0	0	0	0
66	T	1	0	1	1	0.283	2	0.283 ± 0.068	0.006 ± 0.002	0.008	0	0.382 (P > 0.1)
78	B	1	0	1	1	0.107	2	0.107 ± 0.055	0.002 ± 0.001	0.003	0	-0.675 (P > 0.1)
Ia	MHCIa	3	0	3	3	0.907	4	0.649 ± 0.037	0.034 ± 0.004	0.040	0	0.767 (P > 0.1)
Ib	MHCIb	2	0	2	2	0.214	2	0.107 ± 0.055	0.008 ± 0.004	0.010	0	-0.898 (P > 0.1)
Ic	MHCIc	2	0	2	2	0.492	3	0.458 ± 0.066	0.012 ± 0.002	0.011	0.017	0.212 (P > 0.1)
IIa	MHCIIa	2	0	2	2	0.557	3	0.511 ± 0.043	0.019 ± 0.002	0.021	0.011	0.471 (P > 0.1)
IIb	MHCIIb	2	0	2	2	0.423	3	0.297 ± 0.076	0.016 ± 0.004	0.019	0	-0.064 (P > 0.1)

K, average number of pairwise nucleotide differences; H, number of haplotypes; Hd, haplotype diversity; π, observed average pairwise nucleotide diversity; Kn, rate of non-synonymous mutations; Ks, rate of synonymous mutations. ^aB, B-cell epitope; T, T-cell epitope; none, no epitope identified