wgc.md

Whole genome comparison of maize assemblies

November 06, 2018

• Pipeline components:
  • minimap2 was used to align one assembly to another;
  • blat chain/net tools were used to process alignment resuls and build synteny chains/nets;
  • bcftools and GATK4 were used to call variants;
  • snpEff was used to evaluate variant effects on sytenic genes
• whole genome synteny plots
  • Mo17 vs B73
  • W22 vs B73
  • PH207 vs B73
  • PHB47 vs B73
• Table 1. Whole genome alignment statistics.

• Table 2. Summary of variants called by synteny comparison.

• plot of synteny content and variant density
  • Mo17 vs B73
  • W22 vs B73
  • PH207 vs B73
  • PHB47 vs B73
• Table 3. Summary of variant effects on syntenic genes.