Table 2.

Single nucleotide polymorphism statistics

	SNPs unique to a single subspecies		SNPs in both subspecies
	B47	F56	B47 and F56
Total SNP count	38,645	44,800	26,796
Tissue specific SNPs	23,879	25,875	4,083
MSGI 1.2 sequences with SNPs	10,861	11,585	6,749

Single nucleotide polymorphisms (SNPs) unique to each M. sativa subspecies and SNPs identified in both M. sativa subspecies (likely representing allelic variation). Roughly 60 % of SNPs unique to one subspecies are only identified in a single tissue. The number of MSGI 1.2 sequences containing SNPs reveals that each sequence contains multiple SNPs. Details on each SNP can be found in Additional file 10