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 mr1388 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
vg1217569463 sf1217563418 12 17569463 5.23E-09 1.55E-07
vg1217580896 sf1217574851 12 17580896 2.26E-08 2.80E-07
vg0124756770 sf0124755726 1 24756770 4.66E-08 3.14E-06
vg0821373981 sf0821371268 8 21373981 3.08E-07 1.12E-06
vg0610874578 sf0610873579 6 10874578 3.15E-06 3.77E-06