Table 2.

SNP filtering criteria used in walnut SNP discovery

	Item	Initial criteria	Adjusted
1	Minimum read depth mapped to the reference sequences (Minimum RMD)	≥ 5
	Maximum read depth mapped to the reference sequences (maximum RMD)	No constraint	≤ 25 ( $\stackrel{￣}{X}$+ 0.5- s)(a)
2	Folded variant frequency in SOLiD reads (FVF)	≥ 0.2	Statistically no deviation from 0.5(b)
3	Mapping quality score in SAMtools (MQS)	≥ 25	≥ 30
	Reference SNP base quality	SNP base ≥40 for genic BESs and ≥45 for non-genic BESs
4	Removing homopolymer SNPs	SNP base string length ≥ 3 bp
5	Removing very close SNPs	> 3 bp between two contiguous SNPs
6	Removing SNPs at the right side of Sanger reads	> 30 bp away from the right side
7	Illumina genotyping quality	≥ 60 bp between two contiguous SNPs

(a) See the text for definition of $\overline{X}$ and s. (b) See Methods.