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 mr1902 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
vg0724506217 sf0724505223 7 24506217 1.81E-35 3.15E-26
vg0724516475 sf0724515481 7 24516475 2.01E-35 1.08E-25
vg0724585298 sf0724584304 7 24585298 2.73E-12 9.73E-07
vg1117553288 sf1117087144 11 17553288 3.53E-12 NA
vg0331937585 sf0331930462 3 31937585 1.36E-10 NA
vg0103093065 sf0103092065 1 3093065 2.48E-10 NA
vg0724530317 sf0724529323 7 24530317 1.95E-09 1.84E-15
vg1210687991 sf1210685404 12 10687991 4.87E-09 1.78E-06
vg0400998939 sf0400994491 4 998939 6.33E-09 4.82E-06
vg0725325993 sf0725324999 7 25325993 7.21E-09 4.54E-06
vg0714029010 sf0714028017 7 14029010 NA 2.46E-06