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 mr1566 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
vg0819858633 sf0819855920 8 19858633 1.21E-09 NA
vg0301284105 sf0301283103 3 1284105 1.73E-09 NA
vg0322532678 sf0322531167 3 22532678 7.47E-09 NA
vg0307993242 sf0307992180 3 7993242 1.03E-08 8.69E-06
vg0204076184 sf0204076181 2 4076184 7.60E-08 NA
vg1125768032 sf1125301871 11 25768032 3.30E-07 2.53E-07
vg0921539163 sf0921538682 9 21539163 1.23E-06 3.16E-06
vg0405322574 sf0405318015 4 5322574 5.23E-06 NA
vg1106885476 sf1106881221 11 6885476 NA 1.54E-06
vg0906631032 sf0906630032 9 6631032 NA 1.84E-06
vg1211652112 sf1211649448 12 11652112 NA 2.55E-06
vg0802984189 sf0802983192 8 2984189 NA 4.28E-06
vg0402111447 sf0402107041 4 2111447 NA 6.62E-06