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 mr1161 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
vg1007456082 sf1007471705 10 7456082 3.96E-26 3.89E-15
vg0407824609 sf0407819877 4 7824609 4.34E-22 8.63E-07
vg0403206873 sf0403202476 4 3206873 9.09E-22 2.08E-08
vg1007493091 sf1007508714 10 7493091 2.72E-20 5.33E-10
vg1006533973 sf1006549596 10 6533973 4.08E-20 1.07E-10
vg0528707739 sf0528645094 5 28707739 5.62E-20 2.04E-07
vg1009344237 sf1009273058 10 9344237 2.15E-19 2.03E-09
vg0142683989 sf0142682945 1 42683989 3.41E-19 1.02E-06
vg1010146858 sf1010075679 10 10146858 2.77E-17 1.85E-06
vg0110929029 sf0110928005 1 10929029 7.04E-17 2.90E-06
vg0317087788 sf0317086602 3 17087788 NA 3.17E-08
vg0317244657 sf0317243467 3 17244657 NA 1.71E-06
vg0802219948 sf0802218951 8 2219948 NA 2.64E-06