Table 2.

The probe composition and gene targets of Ath.test assay.

Probe name	Probe length	Target genomic site	Locus ID	Predicted CNV status	Source∗
ctrl1	96 nt	Chr1:25593..25645	AT1G01040	Non-variable; normalization control	a
ctrl2	111 nt	Chr4:11476533..11476582	AT4G21580	Non-variable; normalization control	a
ctrl3	124 nt	Chr2:15194440..15194490	AT2G36230	Non-variable; normalization control	a
ctrl4	144 nt	Chr5:7847361..7847414	AT5G23290	Non-variable; normalization control	a
ctrl5	172 nt	Chr1:27465468..27465522	AT1G73010	Non-variable; normalization control	a
mlpaA	160 nt	Chr1:17539289..17539343	AT1G47670	Non-variable	b; c
mlpaB1; mlpaB2	90 nt 148 nt	Chr1:30374276..30374321 Chr1:30373647..30373699	AT1G80830	Non-variable	b; c
mlpaC	93 nt	Chr1:11651708..11651754	AT1G32300	Biallelic	b
mlpaD1; mlpaD2	105 nt 114 nt	Chr1:9575624..9575678 Chr1:9577003..9577055	AT1G27570	Multiallelic	b; c
mlpaE1; mlpaE2	136 nt 196 nt	Chr1:19726669..19726721 Chr1:19727385..19727439	AT1G52950	Multiallelic	b; c
mlpaF1; mlpaF2	99 nt 120 nt	Chr3:7737420..7737467 Chr3:7737872..7737929	AT3G21960	Multiallelic	b; c
mlpaG1; mlpaG2	128 nt 164 nt	Chr4:10641616..10641668 Chr4:10644628..10644679	AT4G19520	Biallelic	c
mlpaH	180 nt	Chr4:13592606..13592658	AT4G27080	Multiallelic	b; c
mlpaI	117 nt	Chr4:17705274..17705327	AT4G37685	Multiallelic	b
mlpaJ1; mlpaJ2	108 nt 156 nt	Chr5:2976409..2976464 Chr5:2978013..2978065	AT5G09590	Multiallelic; part of the gene	c
mlpaK1; mlpaK2	188 nt 102 nt	Chr5:22228424..22228479 Chr5:22229438..22229488	AT5G54710	Multiallelic	b; c
mlpaL	132 nt	Chr5:24796111..24796161	AT5G61700	Multiallelic	c

^∗The initial information about the gene CNV status comes from the following resources: a, Zmienko et al. (2016); b, Arabidopsis 1001 Genomes Project; c, our unpublished analysis of the WGS data originally presented in Cao et al. (2011).