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 mr1836 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
vg1202342821 sf1202341822 12 2342821 1.02E-07 4.00E-08
vg0818041875 sf0818039162 8 18041875 1.52E-07 4.25E-06
vg1107500004 sf1107495749 11 7500004 7.42E-07 3.52E-08
vg0818033565 sf0818030852 8 18033565 2.41E-06 4.30E-06
vg1002370671 sf1002369648 10 2370671 5.62E-06 3.05E-06
vg0706116721 sf0706115722 7 6116721 9.17E-06 NA
vg1106469220 sf1106464972 11 6469220 NA 2.25E-06
vg1213459961 sf1213457299 12 13459961 NA 3.01E-06