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 mr1424 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
vg0206261727 sf0206261727 2 6261727 9.46E-07 9.46E-07
vg1108671225 sf1108665835 11 8671225 1.02E-06 1.02E-06
vg0725376215 sf0725375221 7 25376215 1.43E-06 1.43E-06
vg0906503065 sf0906502065 9 6503065 1.78E-06 1.78E-06
vg1104966080 sf1104961891 11 4966080 1.93E-06 1.93E-06
vg0718838390 sf0718837397 7 18838390 2.75E-06 2.75E-06
vg0720364932 sf0720363939 7 20364932 2.89E-06 2.89E-06
vg1217803999 sf1217775433 12 17803999 3.23E-06 3.23E-06
vg0726962702 sf0726961708 7 26962702 4.40E-06 4.40E-06
vg1106375766 sf1106371518 11 6375766 7.64E-06 7.64E-06