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 mr1014 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
vg0133688513 sf0133687469 1 33688513 2.45E-13 1.11E-11
vg0133596937 sf0133595893 1 33596937 5.35E-12 5.23E-11
vg0217651623 sf0217645753 2 17651623 3.73E-09 NA
vg0133276859 sf0133275815 1 33276859 4.48E-09 5.44E-07
vg0129296429 sf0129295384 1 29296429 4.57E-09 NA
vg1223140018 sf1223106478 12 23140018 6.08E-09 NA
vg0129235291 sf0129234246 1 29235291 1.20E-08 2.08E-06
vg1121667268 sf1121201145 11 21667268 1.49E-06 NA
vg0406828836 sf0406824281 4 6828836 2.56E-06 NA
vg0131505553 sf0131504509 1 31505553 3.80E-06 2.88E-06
vg1207955286 sf1207952692 12 7955286 6.65E-06 NA
vg0527271146 sf0527208502 5 27271146 NA 4.72E-06