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 mr1993 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
vg0418048617 sf0417876658 4 18048617 9.07E-13 1.26E-07
vg0720493129 sf0720492136 7 20493129 9.20E-12 1.50E-06
vg0617827445 sf0617826448 6 17827445 8.01E-11 7.62E-06
vg0613296114 sf0613295115 6 13296114 8.22E-11 NA
vg0324586813 sf0324584892 3 24586813 1.02E-10 2.82E-06
vg0414636138 sf0414626852 4 14636138 1.05E-10 9.25E-07
vg0610930251 sf0610929252 6 10930251 3.86E-08 2.18E-06
vg0335633631 sf0335626500 3 35633631 2.44E-07 NA
vg1220111154 sf1220082596 12 20111154 5.82E-07 2.40E-07
vg0912020992 sf0912019991 9 12020992 1.55E-06 1.11E-06
vg0609450365 sf0609449366 6 9450365 NA 1.66E-06