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 ( <a onClick="popup('http://www.biomedcentral.com/1471-2164/13/354/mathml/M2','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/13/354/mathml/M2">View MathML</a>+ 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 <a onClick="popup('http://www.biomedcentral.com/1471-2164/13/354/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/13/354/mathml/M1">View MathML</a> and s. (b) See Methods.

You et al.

You et al. BMC Genomics 2012 13:354   doi:10.1186/1471-2164-13-354

Open Data