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 mr1195 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
vg0608148241 sf0608147242 6 8148241 8.78E-09 NA
vg0506864701 sf0506864643 5 6864701 2.34E-08 NA
vg1124714625 sf1124248465 11 24714625 2.39E-08 NA
vg1006186534 sf1006202183 10 6186534 4.43E-08 NA
vg1124928261 sf1124462101 11 24928261 6.10E-08 NA
vg1005834536 sf1005851074 10 5834536 2.42E-07 1.86E-06
vg0601639995 sf0601638996 6 1639995 1.89E-06 NA
vg0701305238 sf0701304238 7 1305238 1.93E-06 1.31E-06