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 mr1047 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
vg0910043479 sf0910042478 9 10043479 1.53E-10 NA
vg1216560958 sf1216558251 12 16560958 3.00E-10 NA
vg0434287265 sf0434102159 4 34287265 3.54E-10 8.97E-06
vg0818600655 sf0818597942 8 18600655 5.15E-10 6.58E-06
vg1208635982 sf1208633389 12 8635982 6.66E-10 NA
vg0818860176 sf0818857463 8 18860176 4.30E-08 NA