Table 1.

Genomic frequencies of the SNPs in the HP600 haplotypes in Region01.

SNP	Name	Change	Polymorphism type	Position	Coverage	Variant coverage	Genomic detected	Transcriptome proportion	Missing haplotype for more common SNP				Missing haplotype for variant SNP
									Genomic variant	Genomic	Genomic proportion	P-value (binomial test)	Genomic variant	Genomic	Genomic proportion	P-value (binomial test)
1	C	G -> C	SNP (transversion)	12	443	101	Yes	0.23	1	7	0.125	2.32E-09	2	6	0.25	2.98E-01*
2	–	-C	Deletion	78	515	28	Yes	0.05	1	7	0.125	1.13E-07	2	6	0.25	4.76E-32
3	T	C -> T	SNP (transition)	133	542	38	Yes	0.07	1	7	0.125	5.16E-05	2	6	0.25	1.62E-27
4	A	G -> A	SNP (transition)	153	577	33	Yes	0.06	1	7	0.125	9.76E-08	2	6	0.25	1.56E-34
5	TT	GG -> TT	Substitution	166	699	137	Yes	0.2	1	7	0.125	1.18E-07	2	6	0.25	8.85E-04
6	T	C -> T	SNP (transition)	263	569	55	No	0.1	1	7	0.125	4.23E-02	1	7	0.125	4.23E-02
7		(GAG)3 -> (GAG)2	Deletion (tandem repeat)	283	654	42	No	0.06	1	7	0.125	4.35E-07	1	7	0.125	4.35E-07
8	C	T -> C	SNP (transition)	429	849	83	No	0.1	1	7	0.125	1.68E-02	1	7	0.125	1.68E-02
9	A	G -> A	SNP (transition)	434	993	69	No	0.07	1	7	0.125	1.68E-08	1	7	0.125	1.68E-08
10	C	G -> C	SNP (transversion)	436	1035	275	Yes	0.27	2	6	0.25	2.51E-01*	3	5	0.375	1.196E-13
11	T	G -> T	SNP (transversion)	463	936	56	No	0.06	1	7	0.125	5.11E-11	1	7	0.125	5.11E-11
12	A	C -> A	SNP (transversion)	519	679	57	No	0.08	1	7	0.125	9.10E-04	1	7	0.125	9.10E-04

Genome and transcriptome SNPs were used. The global expression (in diverse tissues) was used to determine whether the genomic frequency could explain the transcription frequency (H₀). The binomial test was used to verify H₀. The

^“*”in p-values reflect the acceptance of H₀.