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Table 2 SNP filtering criteria used in this study

From: Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

  Item Criteria of putative SNPs
1 Reference sequence length ≥ 200 bp
2 Minimum mapped read depth to the reference ≥ 3
  Maximum mapped read depth to the reference Roche 454: ≤ 5
Solexa:≤ 10
SOLiD genomic reads: ≤ 50
SOLiD cDNA: ≤ 100
3 Consensus base ratio ≥ 0.9
4 Mapping quality score in SAMTools ≥ 20
  Reference SNP base quality score and neighborhood quality standard (NQS) score SNP base ≥30
NQS 11 bases: ≥ 20
5 Removing homopolymer SNPs SNP base string length ≥ 3 bp
6 Removing very close SNPs > 3 bp between two contiguous SNPs
7 Removing SNPs at the right side of 454 reads > 30 bp away from the right side
8 Illumina genotyping quality (optional for SNP discovery but recommended for SNPs intended for Illumina GoldenGate assays ) ≥ 60 bp between two contiguous SNPs