Table 4.

Copy number variant validation by quantitative Polymerase Chain Reaction (qPCR)

Chromosome*	Location	Gene†	Gene copy number estimates‡ for four strains
			ALP3	SAF4	SLV1	USA12
5 long	795197	Ds71757	0.92 ± 0.04	1.20 ± 0.15	3.20 ± 0.44*	2.33 ± 0.43*
	764916	Ds71743	0.87 ± 0.03	1.16 ± 0.17	2.91 ± 0.79*	1.84 ± 0.02*
5 short	2546495	Ds72297	2.30 ± 0.16*	1.06 ± 0.05	1.06 ± 0.03	1.07 ± 0.17
	2080702	Ds72172	2.35 ± 0.04*	0.88 ± 0.16	0.86 ± 0.28	0.99 ± 0.15
	1505739	Ds72010	1.92 ± 0.07*	1.06 ± 0.06	0.89 ± 0.03	0.80 ± 0.12
9	914042	Ds157678	1.22 ± 0.02*	2.80 ± 0.72*	1.03 ± 0.36	2.12 ± 0.19*
11	1319989	Ds75320	2.66 ± 0.02*	4.38 ± 0.26*	1.10 ± 0.13	2.30 ± 0.03*
13 long	69203	Ds161036	1.12 ± 0.04	1.18 ± 0.17	1.08 ± 0.10	1.15 ± 0.09
	161624	Ds75737	0.88 ± 0.02	1.02 ± 0.15	0.81 ± 0.06	0.84 ± 0.40
13 short	749433	Ds29553	1.90 ± 0.08*	1.02 ± 0.03	1.03 ± 0.10	1.00 ± 0.05
	828406	Ds75914	2.07 ± 0.08*	1.05 ± 0.15	1.08 ± 0.07	1.35 ± 0.16
14	116999	Ds75967	2.09 ± 0.00*	2.21 ± 0.15*	1.15 ± 0.03	1.89 ± 0.02*

^*Chromosome of Dothistroma septosporum NZE10 to which reads from the other strains were mapped.

^†Target genes for qPCR, located in regions predicted by CNVnator to be duplicated (Table S6).

^‡Mean ± standard deviation (SD) gene copy number estimate determined by qPCR compared to the single copy gene AflR and normalized to the genome reference strain NZE10. Significantly higher target/reference ratios compared to NZE10 are indicated with an asterisk (P < 0.01). Dark grey shading indicates CNVnator prediction of entire chromosome duplication (or long/short section of chromosome 5 or 13); light grey shading indicates partial duplication (see Table S6).