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 mr1002 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
vg1207888547 sf1207885953 12 7888547 1.20E-32 3.01E-19
vg0727588197 sf0727587203 7 27588197 3.43E-15 NA
vg0301511076 sf0301510073 3 1511076 5.17E-15 NA
vg0805899713 sf0805898716 8 5899713 2.82E-14 NA
vg0131734945 sf0131733901 1 31734945 4.68E-14 NA
vg0335139941 sf0335132811 3 35139941 1.38E-12 2.60E-07
vg0133389825 sf0133388781 1 33389825 1.39E-07 NA
vg0334584062 sf0334576932 3 34584062 NA 8.92E-09
vg0810439225 sf0810438229 8 10439225 NA 1.56E-08
vg1207428614 sf1207426021 12 7428614 NA 4.98E-07
vg0301938071 sf0301937067 3 1938071 NA 4.05E-06