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 mr1185 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
vg1105907265 sf1105903017 11 5907265 3.21E-09 2.00E-06
vg0919811754 sf0919811273 9 19811754 4.17E-09 NA
vg0919811177 sf0919810696 9 19811177 4.97E-09 NA
vg0431443433 sf0431258331 4 31443433 1.16E-08 NA
vg0919872267 sf0919871786 9 19872267 3.12E-08 3.20E-06
vg0413443781 sf0413434495 4 13443781 4.01E-08 3.99E-07
vg1127411416 sf1126939803 11 27411416 4.90E-08 1.83E-06
vg0412475075 sf0412465790 4 12475075 2.12E-07 9.82E-06
vg0922613922 sf0922613441 9 22613922 1.41E-06 1.67E-06
vg0715691039 sf0715690046 7 15691039 3.30E-06 NA