TABLE 4.

Single nucleotide variants associated with eBL^a

Gene	Position	Ref	Alt	AA change	eBLs		Healthy controls		P	OR
					Genotypes	Alt count	Genotypes	Alt count
EBNA2	37668	T	C	S485P	54	24	36	2	0.000328	0.1
EBNA1	95773	A	T	N38Y	57	3	36	11	0.001322	6.67213
EBNA1	95778	T	G	H39Q	57	3	37	12	0.000538	7.16129
BcLF1	124703	T	G	K159T	56	1	34	7	0.003178	12.7377
BcLF1	124709	G	A	A157V	56	1	34	7	0.003092	12.7377
BARF1	165131	T	C	V29A	57	36	36	10	0.004082	0.349462

^aA single nucleotide variant association test results with P < 0.01 after type stratification. The table summarizes the statistically significant single nucleotide variant associations and their effects in the coding regions. Reference (Ref) refers to the genotype based on the consensus of all genomes in the sequencing set, and the variant position denotes the projection to the type 1 reference genome (NC_007605). An association test was performed for every variant position comparing the frequency of reference and alternative (minor allele) bases among eBL patient and healthy control children (Fisher exact test). Empirical P values are based on one million permutations. For the genotypes, genomes with missing data (Ns, lack of coverage) were excluded. Ref, reference allele; Alt, alternative/variant allele; AA, amino acid; OR, odds ratio.