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 mr1526 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
vg0609990520 sf0609989521 6 9990520 2.04E-07 2.04E-07
vg1004538986 sf1004555524 10 4538986 3.85E-07 3.85E-07
vg1126793847 sf1126322234 11 26793847 3.98E-07 3.98E-07
vg1004381963 sf1004398501 10 4381963 4.01E-07 4.02E-07
vg0118489802 sf0118488756 1 18489802 4.63E-07 4.63E-07
vg1126091011 sf1125619425 11 26091011 5.92E-07 5.92E-07
vg0608359756 sf0608358757 6 8359756 6.26E-07 6.26E-07
vg0616129303 sf0616128305 6 16129303 8.02E-07 8.02E-07
vg0713293448 sf0713292455 7 13293448 8.72E-07 8.72E-07
vg1121393340 sf1120927217 11 21393340 1.09E-06 1.09E-06
vg0610489279 sf0610488280 6 10489279 1.10E-06 1.10E-06
vg0124948510 sf0124947466 1 24948510 1.15E-06 1.15E-06
vg0414121081 sf0414111796 4 14121081 1.26E-06 1.26E-06
vg0900715492 sf0900714492 9 715492 1.36E-06 1.36E-06
vg0427974731 sf0427789595 4 27974731 1.64E-06 1.64E-06
vg1215514024 sf1215511321 12 15514024 1.94E-06 1.94E-06
vg1122427075 sf1121960946 11 22427075 2.38E-06 2.38E-06
vg0409847596 sf0409838294 4 9847596 2.79E-06 2.79E-06
vg0410412648 sf0410403347 4 10412648 3.01E-06 3.01E-06
vg0433017442 sf0432832328 4 33017442 3.09E-06 3.09E-06
vg0808407654 sf0808406658 8 8407654 3.30E-06 3.30E-06
vg0808407675 sf0808406679 8 8407675 3.88E-06 3.88E-06