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 mr1010 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
vg0433794465 sf0433609350 4 33794465 1.00E-17 1.00E-08
vg0300922282 sf0300921280 3 922282 5.51E-15 NA
vg0136958261 sf0136957218 1 36958261 1.10E-14 NA
vg0826352073 sf0826349359 8 26352073 1.12E-14 NA
vg1102357540 sf1102353399 11 2357540 4.23E-14 NA
vg0907789558 sf0907788558 9 7789558 1.51E-12 2.37E-06
vg1105297664 sf1105293415 11 5297664 1.36E-10 1.95E-06
vg1126752035 sf1126280422 11 26752035 1.89E-10 4.65E-06
vg0433948721 sf0433763617 4 33948721 NA 6.74E-07
vg0909064717 sf0909063716 9 9064717 NA 2.57E-06
vg0501672160 sf0501672144 5 1672160 NA 4.24E-06
vg0908951187 sf0908950186 9 8951187 NA 4.31E-06