Skip to main content

Advertisement

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).