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
vg0610648813 sf0610647814 6 10648813 6.00E-17 4.65E-14
vg0610684751 sf0610683752 6 10684751 1.25E-15 1.10E-13
vg0610489279 sf0610488280 6 10489279 1.49E-09 8.35E-07
vg0403922278 sf0403917884 4 3922278 1.74E-09 9.96E-08
vg0610435197 sf0610434198 6 10435197 3.61E-09 2.56E-07
vg0626895745 sf0626894748 6 26895745 3.31E-08 1.48E-07
vg0611689492 sf0611688493 6 11689492 5.12E-08 NA
vg0626882641 sf0626881644 6 26882641 9.10E-08 1.23E-07
vg0717900558 sf0717899565 7 17900558 2.83E-07 2.50E-06
vg1205756282 sf1205755264 12 5756282 2.90E-06 2.11E-06