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 mr1062 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
vg0405913502 sf0405908943 4 5913502 7.00E-13 2.86E-09
vg0409367144 sf0409357843 4 9367144 2.87E-11 1.03E-06
vg1011999393 sf1011928208 10 11999393 2.92E-10 1.12E-06
vg0412697916 sf0412688627 4 12697916 8.93E-10 7.66E-06
vg0402016354 sf0402011950 4 2016354 1.12E-09 3.80E-08
vg1213038870 sf1213036209 12 13038870 1.69E-09 4.59E-06
vg0405536257 sf0405531698 4 5536257 1.98E-08 1.04E-07
vg0903736728 sf0903735728 9 3736728 7.28E-08 8.47E-07
vg1104193419 sf1104189321 11 4193419 1.54E-07 1.37E-06
vg1122445799 sf1121979670 11 22445799 1.59E-06 1.25E-06
vg1207276357 sf1207273764 12 7276357 9.51E-06 2.34E-06
vg1216729892 sf1216723846 12 16729892 NA 8.31E-08
vg0402529380 sf0402524985 4 2529380 NA 1.47E-06