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Table 2 SNP filtering criteria used in walnut SNP discovery

From: Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms

  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 (+ 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  
  1. (a) See the text for definition of X ¯ and s. (b) See Methods.