Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat

BMC Genomics

Table 1 Summary statistics for homoeologue-specific variants (HSVs) in euploid wheat

Chrom group	Reference transcriptome length (bp)	RNA-Seq coverage^a	Number (%) of 2-allele HSVs diagnostic for homoeolocus			P value^b	Number (%) of 3-allele HSVs	Total HSVs	HSV density^c
			A	B	D
1	505,132	540 X	2,611	2,830	1,883	1.89x10^-44	97	7,421	0.015
1	505,132	540 X	(35.2)	(38.1)	(25.4)	1.89x10^-44	(1.3)	7,421	0.015
5	567,044	860 X	2,905	2,837	2,710	0.031	94	8,546	0.015
5	567,044	860 X	(34.0)	(33.2)	(31.7)	0.031	(1.1)	8,546	0.015
Total	1,072,176	700 X	5,516	5,667	4,593	1.21x10^-28	191	15,776	0.015
Total	1,072,176	700 X	(34.5)	(35.5)	(28.8)	1.21x10^-28	(1.2)	15,776	0.015

^aCoverage is given as the average number of quality filtered reads aligned per site using novoalign software, from all euploid Chinese Spring wheat samples.
^bp for a chi-square test of equal numbers of 2-allele HSVs diagnostic for each homoeolocus.
^cHSV density is given as the average number of variants per site.

ISSN: 1471-2164