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 mr1094 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
vg0610609054 sf0610608055 6 10609054 5.74E-13 1.53E-10
vg0610648813 sf0610647814 6 10648813 1.31E-12 5.46E-11
vg0610343438 sf0610342439 6 10343438 4.32E-10 2.23E-08
vg0610372153 sf0610371154 6 10372153 2.51E-09 1.90E-08
vg0403922278 sf0403917884 4 3922278 2.91E-08 1.22E-06
vg1220952777 sf1220919326 12 20952777 4.73E-08 NA
vg1004372674 sf1004389212 10 4372674 6.25E-08 2.77E-06
vg1004372914 sf1004389452 10 4372914 2.77E-07 2.73E-06