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 mr1499 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
vg0726795981 sf0726794987 7 26795981 2.11E-07 2.11E-07
vg1126117539 sf1125645953 11 26117539 3.06E-07 3.06E-07
vg1125417163 sf1124951002 11 25417163 3.09E-07 3.09E-07
vg0107711388 sf0107710388 1 7711388 3.17E-07 3.17E-07
vg1122371090 sf1121904961 11 22371090 3.76E-07 3.76E-07
vg0908132614 sf0908131614 9 8132614 4.53E-07 4.53E-07
vg0908143257 sf0908142257 9 8143257 9.69E-07 9.69E-07
vg0707146260 sf0707145265 7 7146260 3.92E-06 3.92E-06
vg0203808446 sf0203808443 2 3808446 4.10E-06 4.10E-06
vg0912925804 sf0912924803 9 12925804 4.34E-06 4.34E-06