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 mr1194 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
vg0100543265 sf0100542265 1 543265 3.74E-10 9.54E-07
vg0525944770 sf0525882191 5 25944770 5.40E-10 4.00E-06
vg0414249163 sf0414239876 4 14249163 6.49E-10 1.18E-07
vg0809743223 sf0809742227 8 9743223 6.72E-09 NA
vg0133432014 sf0133430970 1 33432014 1.66E-08 NA
vg0906746271 sf0906745271 9 6746271 6.93E-07 2.72E-07
vg0812490623 sf0812489527 8 12490623 7.91E-07 NA
vg0225159946 sf0225154077 2 25159946 NA 3.95E-06