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 mr1812 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
vg0902107236 sf0902106236 9 2107236 1.62E-09 3.49E-07
vg0220342715 sf0220336847 2 20342715 3.14E-09 5.78E-06
vg1020531763 sf1020460242 10 20531763 5.17E-09 1.24E-06
vg0805992743 sf0805991746 8 5992743 6.27E-09 5.14E-06
vg0801628860 sf0801627862 8 1628860 8.30E-09 NA
vg0620734924 sf0620733927 6 20734924 4.35E-07 1.03E-06
vg0420718113 sf0420546156 4 20718113 6.61E-07 2.99E-07
vg1209946884 sf1209944294 12 9946884 4.97E-06 3.94E-06
vg1215307750 sf1215305048 12 15307750 6.64E-06 3.24E-06
vg0902278490 sf0902277490 9 2278490 NA 7.21E-07
vg0235581681 sf0235575812 2 35581681 NA 1.92E-06