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 mr1832 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
vg0220342715 sf0220336847 2 20342715 2.63E-08 2.80E-06
vg0805992743 sf0805991746 8 5992743 9.06E-08 3.44E-06
vg1020531763 sf1020460242 10 20531763 1.18E-07 1.12E-06
vg0223525077 sf0223519208 2 23525077 2.61E-07 2.83E-06
vg1215307750 sf1215305048 12 15307750 4.88E-07 1.58E-06
vg0420718113 sf0420546156 4 20718113 5.19E-07 7.98E-07
vg1209946884 sf1209944294 12 9946884 9.49E-07 1.73E-06
vg0817557507 sf0817554793 8 17557507 1.87E-06 4.80E-06
vg0715026108 sf0715025115 7 15026108 3.53E-06 6.24E-06
vg0902278490 sf0902277490 9 2278490 NA 1.83E-06
vg0620734924 sf0620733927 6 20734924 NA 2.91E-06