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 mr1677 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
vg0907750844 sf0907749844 9 7750844 1.42E-10 1.19E-09
vg0709922564 sf0709921570 7 9922564 3.89E-09 1.10E-07
vg0622754629 sf0622753632 6 22754629 9.27E-09 3.02E-07
vg0619058753 sf0619057756 6 19058753 5.97E-08 5.74E-06
vg0618969958 sf0618968961 6 18969958 3.76E-07 4.28E-06
vg0105146788 sf0105145788 1 5146788 4.03E-07 3.59E-06
vg0600222950 sf0600221950 6 222950 4.36E-06 4.61E-06
vg0129870980 sf0129869935 1 29870980 NA 3.75E-06
vg1218543377 sf1218514813 12 18543377 NA 3.79E-06