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 mr1157 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
vg1012367119 sf1012295934 10 12367119 3.39E-08 1.10E-06
vg1012428033 sf1012356848 10 12428033 6.74E-08 7.45E-07
vg0900731282 sf0900730282 9 731282 7.26E-08 6.40E-06
vg1212132495 sf1212129831 12 12132495 9.89E-08 6.69E-06
vg0820694826 sf0820692113 8 20694826 1.78E-07 3.57E-07
vg0820098280 sf0820095567 8 20098280 2.22E-07 7.99E-07
vg1117996451 sf1117530309 11 17996451 4.47E-06 3.67E-06