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 mr1835 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
vg0729424427 sf0729423435 7 29424427 4.87E-09 8.17E-08
vg1117628825 sf1117162681 11 17628825 7.64E-09 1.53E-06
vg1005346841 sf1005363378 10 5346841 9.00E-08 NA
vg0408392718 sf0408387992 4 8392718 1.75E-07 2.67E-06
vg0527177720 sf0527115076 5 27177720 2.03E-07 4.58E-06
vg0811767202 sf0811766207 8 11767202 2.16E-07 1.27E-06
vg1217374273 sf1217368228 12 17374273 6.01E-07 4.03E-07