Genotype Data Download

T3/Wheat

Large protocols
ProtocolDownload
genotype project
description
Exome capture HapMap2019 HapMap 337 accessions, 7.5M markers meta data
Exome capture Diversity2019_Diversity 1000 accessions, Passport
Exome capture WatkinsWatkins Core 2017 meta data
MRASeq RGONRGON 2023
Exome capture PHG472PHG472

Imputed protocols and projects
Method: Practical Haplotype Graph - PHG V2 with 2.9M markers
Visualize: JBrowse
Description: Imputation pipeline and accuracy
ProtocolDownload
genotype project
accessionsCluster with PHGImputation accuracy
vs 2019_HapMap
Infinium 90K v2.1 TCAP90K_HWWAMP29596% - details
TCAP90K_SpringAM_panel245 81% - details
TCAP90K_YQV14216 95% - details
TCAP90K_CSRVAL14116 PCAna
VRND4_UCD_201576 PCAna
TCAP90K_NAMparents_panel56 88% - details
TCAP90K_HWWAMP_SRPN16 96% - details
TCAP90K_SWWpanel313 91% - details
TCAP90K_LeafRustPanel335 96% - details
TCAP90K_SNBWWW266 PCAna
Infinium 9K v2.1 NSGCwheat9K_4X542 PCAna
WorldwideDiversityPanel_9K2255
GMS v2.1 2021_GMS28882% - details
MRASeq RPN RPN_202086PCA 84% - details
RPN_202190PCA 83% - details
RPN_202280PCA 83% - details
RPN_202388PCA 83% - details
RPN_2020-23286PCA 84% - details
RPN_2020-21157PCA 84% - details
RPN_2021-22150PCA - details
RPN_2022-23151PCA - details
MRASeq RGON RGON_2021300PCA 84% - details
RGON_2022327PCA 84% - details
RGON_2023412PCA 84% - details
Notes:
1. Cluster analysis for Infinium calculated by merging unimputed data with PHG genotypes (common markers).
2. Cluster analysis for other protocols (no common markers) calculated on the unimputed data and showing which accessions are in the PHG
3. Imputation accuracy calculated by comparing every 30th marker between imputed output and 2019_HapMap for matching accessions

T3/Oat

Infinium 2010 genotype protocol Infinium 2010 POGI_ALL.vcf
POGI_2015_Aberdeen.vcf
POGI_2015_ENCORE.vcf
POGI_2015_Other.vcf
POGI_2015_SDSU.vcf
POGI_2015_SOAP.vcf
POGI_2015_UCDavis.vcf
POGI_2015_UIL.vcf
POGI_2015_UMN.vcf
POGI_2015_UOPN.vcf
POGI_2015_UWM.vcf

PepsiCo_OT3098_v2_gene_annotations.gff3
PepsiV2.map - map of 123,141 POGI markers to PepsiCo_OT3098_v2
PepsiV2.GFF - haplotypes of 123,141 POGI markers with map

T3/Barley

Morexv3 gene annotations
BRIDG6 GBS 2019 - Full BRIDG6 NAM population, 178GB