Table 3.

Correlation between SNP Genomic Dosage and Relative Expression Level of TOR and PHYC Haplotypes

				Haplotype dosage (Genomic data)		Read counts RNA-seq		RNA-seq depth (# mapped reads)	Haplotype relative dosage (gDNA)		Haplotype relative expression (mRNA)		Exact binomial test p-value	Haplotypes with alternative SNP
Gene	SNP position	Main haplotype	Alternative haplotype	Main haplotype	Alternative haplotype	Main haplotype	Alternative haplotype		Main haplotype	Alternative haplotype	Main haplotype	Alternative haplotype		030H10	214B20	187L21	102H05	007C22	043C15	156D23
TOR	5463	C	T	6	1	34	6	40	0.86	0.14	0.85	0.15	0.823				X
	5887	G	A	5	2	48	18	66	0.71	0.29	0.73	0.27	0.892						X	X
	6315	G	A	6	1	30	1	31	0.86	0.14	0.97	0.03	0.117						X
	6604	A	T	6	1	65	9	74	0.86	0.14	0.88	0.12	0.740		X
	6646	G	T	5	2	44	15	59	0.71	0.29	0.75	0.25	0.667						X	X
	6924	C	T	6	1	96	11	107	0.86	0.14	0.90	0.10	0.271		X
	7295	T	C	4	3	102	67	169	0.57	0.43	0.60	0.40	0.437					X	X	X
	7356	C	T	6	1	216	0	216	0.86	0.14	1.00	0.00	7.84E-15					X
	7380	T	C	4	3	117	58	175	0.57	0.43	0.67	0.33	0.009					X	X	X

				Haplotype dosage (Genomic data)		Read counts RNA-seq		RNA-seq depth (# mapped reads)	Haplotype relative dosage (gDNA)		Haplotype relative expression (mRNA)		Exact binomial test p-value	Haplotypes with alternative SNP
Gene	SNP position	Main haplotype	Alternative haplotype	Main haplotype	Alternative haplotype	Main haplotype	Alternative haplotype		Main haplotype	Alternative haplotype	Main haplotype	Alternative haplotype		095E16	173M11	038J02	056J11
PHYC	2484	G	T	2	2	30	24	54	0.50	0.50	0.56	0.44	0.497	X	X
	2531	C	T	3	1	52	15	67	0.75	0.25	0.78	0.22	0.675			X
	2619	T	C	3	1	99	0	99	0.75	0.25	1.00	0.00	7.48E-13		X
	2871	G	A	2	2	62	64	126	0.50	0.50	0.49	0.51	0.929			X	X
	2961	A	G	3	1	139	3	142	0.75	0.25	0.98	0.02	6.18E-14				X
	3207	G	A	3	1	86	1	87	0.75	0.25	0.99	0.01	9.03E-10				X
	3353	T	C	3	1	110	2	112	0.75	0.25	0.98	0.02	1.48E-11				X

Note.—Gray filled cells indicate statistically significant correlation between the genomic dosage of SNP loci and the SNP RNA-seq frequency (P-value < 0.05, Exact Binomial Test). “X” indicates the haplotypes containing the alternative SNP.