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 mr1914 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
vg0216929727 sf0216923857 2 16929727 5.37E-14 5.37E-14
vg0316514100 sf0316512745 3 16514100 6.82E-09 6.82E-09
vg0316513657 sf0316512302 3 16513657 7.91E-09 7.91E-09
vg0517773335 sf0517712821 5 17773335 2.90E-08 2.90E-08
vg0210828426 sf0210828424 2 10828426 1.37E-07 1.37E-07
vg0620867473 sf0620866476 6 20867473 2.68E-07 2.68E-07
vg0618883511 sf0618882514 6 18883511 2.72E-07 2.72E-07
vg0216565123 sf0216559253 2 16565123 3.00E-07 3.00E-07
vg0507480268 sf0507480210 5 7480268 8.92E-07 8.93E-07
vg0210369537 sf0210369535 2 10369537 1.32E-06 1.32E-06
vg0430949013 sf0430763893 4 30949013 1.46E-06 1.46E-06
vg1220023538 sf1219994980 12 20023538 2.07E-06 2.07E-06
vg0825088869 sf0825086155 8 25088869 3.78E-06 3.78E-06
vg0218555416 sf0218549547 2 18555416 4.12E-06 4.12E-06
vg0429867566 sf0429682436 4 29867566 4.51E-06 4.52E-06