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 mr1667 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
vg1125548017 sf1125081856 11 25548017 3.51E-23 7.09E-12
vg1125470914 sf1125004753 11 25470914 3.59E-20 3.53E-12
vg0713260653 sf0713259660 7 13260653 1.89E-16 1.05E-07
vg0501932429 sf0501932411 5 1932429 3.51E-16 2.80E-06
vg0514949605 sf0514892148 5 14949605 9.16E-16 NA
vg1123627766 sf1123161636 11 23627766 1.37E-15 1.41E-06
vg0713262120 sf0713261127 7 13262120 5.16E-15 4.79E-08
vg0912193101 sf0912192100 9 12193101 1.12E-14 NA
vg0612544928 sf0612543929 6 12544928 1.59E-12 1.66E-06
vg1125547759 sf1125081598 11 25547759 NA 5.16E-07
vg1127573927 sf1127102314 11 27573927 NA 5.71E-07
vg1125611024 sf1125144863 11 25611024 NA 9.80E-07
vg1125572352 sf1125106191 11 25572352 NA 1.23E-06
vg1126252192 sf1125780606 11 26252192 NA 2.71E-06