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 mr1817 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
vg0141973203 sf0141972160 1 41973203 6.48E-08 NA
vg1018469105 sf1018397662 10 18469105 9.58E-08 NA
vg0700639795 sf0700638795 7 639795 2.31E-07 6.77E-06
vg0324748140 sf0324746219 3 24748140 1.46E-06 4.32E-06
vg1003340954 sf1003339931 10 3340954 8.24E-06 NA
vg1204294640 sf1204293628 12 4294640 NA 2.26E-06
vg1221363597 sf1221330144 12 21363597 NA 3.96E-06