Table 3. Mapping of reads to a reference genome lacking one or more homoeologues of the target gene.

			Line C6		Line A6		Line D3
Target	Hom.	Posn.	Coverage	Allele frequency	Coverage	Allele frequency	Coverage	Allele frequency
GA20ox-A1	ABD	1018	15	1	32	0	66	0
	AB	1018	41	0.34	61	0	123	0
	AD	1018	20	0.75	35	0	74	0
	A	1018	46	0.3	64	0	131	0
GA20ox-B1	ABD	7396	20	0	13	1	48	0
	AB	7396	24	0	17	0.76	57	0
	BD	7396	20	0	13	1	49	0
	B	7396	35	0	32	0.41	112	0
GA20ox-D1	ABD	5981	33	0	21	0	37	1
	AD	5981	33	0	21	0	37	1
	BD	5981	34	0	22	0	38	0.97
	D	5981	35	0	26	0	47	0.79
	BD	6368	38	0.26	58	0	121	0
	D	6368	39	0.26	58	0	123	0

Captured reads from lines C6, A6 and D3, containing homozygous mutations in GA20ox1 homoeologues A, B and D, respectively, were mapped to a reference genome (IWGSC reduced set from Ensembl v21) containing one, two or three of the homoeologous GA20ox1 genes. Numbers in bold indicate dilution of variant reads by reads from homoeologues absent from the reference; numbers in bold italics indicate variant reads from the A genome mis-mapped to the D genome in the absence of the GA20ox1-A1 reference contig. Hom: homoeologue(s) present in the reference; Posn: position in the reference contig; Allele frequency: proportion of variant reads.