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 mr1356 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
vg0300249514 sf0300248514 3 249514 2.02E-07 2.02E-07
vg0820421005 sf0820418292 8 20421005 2.41E-07 2.41E-07
vg1109949998 sf1109944575 11 9949998 3.06E-07 3.06E-07
vg1214600105 sf1214597445 12 14600105 4.34E-07 4.35E-07
vg0431655631 sf0431470524 4 31655631 9.38E-07 9.38E-07
vg1005046900 sf1005063437 10 5046900 1.61E-06 1.61E-06
vg1107375253 sf1107370998 11 7375253 2.38E-06 2.38E-06
vg1214822308 sf1214819649 12 14822308 2.47E-06 2.47E-06
vg0108674689 sf0108673689 1 8674689 3.35E-06 3.35E-06
vg1214815608 sf1214812949 12 14815608 3.41E-06 3.41E-06
vg0103392356 sf0103391356 1 3392356 4.06E-06 4.06E-06
vg1210707069 sf1210704482 12 10707069 4.11E-06 4.11E-06
vg0433638267 sf0433453150 4 33638267 4.62E-06 4.62E-06
vg1210526233 sf1210523646 12 10526233 4.80E-06 4.80E-06