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 mr1419 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
vg1012362305 sf1012291120 10 12362305 7.16E-07 7.16E-07
vg0820873126 sf0820870413 8 20873126 1.31E-06 1.31E-06
vg1104978749 sf1104974560 11 4978749 1.42E-06 1.42E-06
vg1106375766 sf1106371518 11 6375766 1.93E-06 1.93E-06
vg0606257601 sf0606256602 6 6257601 2.52E-06 2.52E-06
vg1216966466 sf1216960420 12 16966466 2.66E-06 2.66E-06
vg0820510689 sf0820507976 8 20510689 4.08E-06 4.08E-06