Intermediate files required for analysis of data associated with EL57 population. (Select and Sequence (SnS) of a segregating sugar beet population provides genomic perspective of host resistance to seedling Rhizoctonia solani infection)

Methods can be found in the paper:

Select and Sequence (SnS) of a segregating sugar beet population provides genomic perspective of host resistance to seedling Rhizoctonia solani infection

Paul Galewski , Andrew Funk and J Mitchell McGrath
Front. Plant Sci. doi: 10.3389/fpls.2021.785267

Description of files:

AlleleFreq.txt - Allele frequency data for resistant, susceptible and unselected beet populations.

Biallelic.vcf - Filtered vcf with only the biallelic sites used for analysis.

DeltaAF.txt  - Changes in allele frequency between seleted and unseleted beet populations

DeltaAF_Signifiant.txt  -  Significant changes in allele frequency between seleted and unseleted beet populations

FST.txt  - Divergence between beet populations selected for Rhizoctonia resistance

Manta_SV.vcf -  Structural variation detected using the program Manta

FST_24.txt  - Fst calculated within a 24bp sliding window

Multiallelic.vcf  - Multiallelic variation, not used in statistical analysis but importnat to understanding causal variation

SNPeff.vcf - vcf file annotated using SNPeff

EL10_2_final_assembly.fa - EL10.2 referance sequence

EL10_2_final_protien.fasta - EL10.2 protien sequences

EL10_2_final_cDNA.fasta - EL10.2 cDNA sequences

EL10_2_final.gff - EL10.2 referance annotation (Liftoff from EL10.1)