Reports GWAS

GWAS Results

For each assembly the follow analysis was run

• Markers aligned to assembly using BLAST
  1. blast-iwgsc.php
  2. parse-blast.php
  • reads BLAST output
  • writes significant matches to blast.results.txt
  3. load-marker-report.php
  • reads blast.results.txt
  • adds marker_uid
  • writes best match for each marker to file marker-report.csv for loading into database table marker_report_reference
• Markers assigned to nearest gene (within 1MB)
  1. get-gene-RefSeq.php
  • reads gene information from gff3 file
  • reads location information from specified physical map
  • writes marker, location, and gene information to table qtl_annotations