Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1375 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0137832701 sf0137831658 1 37832701 1.29E-10 2.29E-08
vg0134507631 sf0134506588 1 34507631 1.57E-09 5.25E-07
vg0630078359 sf0630077361 6 30078359 1.36E-08 5.17E-07
vg1205699592 sf1205698574 12 5699592 3.94E-08 3.68E-06
vg1119202978 sf1118736666 11 19202978 7.20E-08 NA
vg1205465375 sf1205464361 12 5465375 2.06E-06 4.60E-06
vg0801461338 sf0801460340 8 1461338 3.41E-06 2.44E-06