Table 5.

Total and non-synonymous SNPs in the pfam01617 superfamily and genes encoding candidate vaccine antigens. SNPs – the number of nucleotide positions in each gene with high-confidence changes in at least one other strain (excluding gene segments previously defined as absent). NS – the number of SNPs producing a non-synonymous change in at least one strain. Ave. Freq. – average frequency of reads with each SNP across all strains. Ave Cov. – average coverage at each SNP nucleotide position.

	Florida				St. Maries
	SNPs	NS changes	Ave. Freq.	Ave. coverage	SNPs	NS changes	Ave. Freq.	Ave. coverage
omp1(AM1139)	26	11	99.8	65.8	26	11	99.8	71.9
omp2(AM1156)	1	0	100	12	0	0	N/A	N/A
omp3(AM1159)	2	2	100	41	1	1	100	70
omp4(AM1164)	8	2	99.8	43.5	6	0	99.7	58.9
omp5(AM1166)	23	2	99.7	53.9	15	6	99.9	83.2
omp6(AM1219)	5	1	100	68	5	1	90.7	104
omp7(AM1220)	52	11	99.8	13.3	68	27	96.4	33.9
omp8(AM1221)	38	9	93.2	47.2	49	16	96.9	40.4
omp9(AM1222)	32	9	98.3	17.2	31	9	97.7	31.4
omp10(AM1223)	15	10	99.3	35	15	10	99.7	67.9
omp11(AM1255)	26	13	99.8	36	19	10	99.9	30.2
omp12(AM1257)	16	5	99.2	31	17	6	99.3	48.9
omp13(AM1258)	19	8	99.7	21.1	14	5	99.3	70.2
omp14(AM075)	17	7	99.2	75.7	24	12	100	55.1
omp15(AM987)	8	5	100	10.3	4	2	99.3	107.7
opag1(AM1143)	1	0	100	12	2	2	100	160
opag2(AM1142)	4	2	100	77.8	6	4	100	105.2
opag3(AM1140)	43	15	99.8	94.3	43	41	99.8	94.3
msp4(AM090)	8	0	99.8	58.1	9	1	99.1	42.9
AM779	7	1	100.0	37.1	7	1	100.0	37.1
AM780	8	4	96.9	14.1	31	14	99.2	41.7
pal(AM854)	5	3	99.7	60.2	4	2	100.0	58.0
purD(AM1011)	29	1	99.4	42.5	30	1	99.5	48.8
virB3(AM815)	0	0	N/A	N/A	0	0	N/A	N/A
virB4-1(AM814)	8	1	98.5	37.5	4	1	97.2	18.9
virB4-2(AM1053)	8	1	98.5	37.5	4	1	97.2	18.9
virB6(AM811)	46	26	99.6	36.7	46	25	99.6	39.5
virB8-1(AM1316)	2	0	100	35.3	2	0	100	35
virB9-2(AM1315)	2	0	97.4	45	2	0	97.4	35
virB10(AM1314)	5	2	99.9	57.9	5	2	99.9	51.4
virB11(AM1313)	14	1	99.1	52.7	15	1	98.8	46.4