Table 2 SNP filtering criteria used in this study
| Â | 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 |