| 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 |  |