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 mr1135 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
vg0137919286 sf0137918243 1 37919286 6.84E-18 1.09E-13
vg0137930974 sf0137929931 1 37930974 1.54E-17 8.60E-14
vg0811905123 sf0811904128 8 11905123 1.14E-08 NA
vg0138695323 sf0138694280 1 38695323 2.41E-08 NA
vg0108147243 sf0108146243 1 8147243 1.05E-07 1.49E-06
vg0514257018 sf0514199561 5 14257018 2.14E-07 3.73E-06
vg0714431042 sf0714430049 7 14431042 1.70E-06 2.42E-06
vg0425798257 sf0425613121 4 25798257 2.92E-06 4.19E-06
vg1017910378 sf1017839150 10 17910378 NA 1.07E-06
vg0803630208 sf0803629211 8 3630208 NA 1.54E-06