Skip to main content

Table 7 High-quality SNPs identified from the walnut genome after applying the new filters of read mapping depth (≤ 25), SNP mapping quality score (≥ 30), and folded variantfrequency (statistically not different from 0.5)

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

BES

No of BESs

No of BESs with SNPs

Total SNPs

Number of contigs with SNPs

Predicted true SNP rate(a)

Genic

29,223

6,317

8,237

629

87.1%

Non-genic

19,438

3,996

5,202

601

90.0%

Total

48,661

10,313

13,439

677

88.2%

  1. (a) Estimated based on the logistic regression model in 2,765 validated SNPs (Table 6).