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 mr1300 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
vg1000757961 sf1000756937 10 757961 1.74E-18 1.30E-13
vg0528146502 sf0528083857 5 28146502 1.88E-12 1.63E-08
vg1008205459 sf1008134321 10 8205459 1.98E-10 2.16E-06
vg1005270327 sf1005286864 10 5270327 1.20E-09 3.81E-07
vg1128801387 sf1128278166 11 28801387 1.60E-09 NA
vg0706566801 sf0706565806 7 6566801 1.75E-08 2.23E-07
vg1125047295 sf1124581135 11 25047295 1.01E-07 1.16E-06
vg1004990336 sf1005006873 10 4990336 1.16E-07 3.54E-06
vg1125090609 sf1124624449 11 25090609 NA 6.12E-10
vg1125117714 sf1124651554 11 25117714 NA 2.31E-09