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 mr1666 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
vg0407737736 sf0407733003 4 7737736 7.27E-08 7.28E-08
vg1126583494 sf1126111909 11 26583494 4.39E-07 4.40E-07
vg0516203079 sf0516145561 5 16203079 5.94E-07 5.94E-07
vg0503166060 sf0503166036 5 3166060 1.04E-06 1.04E-06
vg0424988358 sf0424803219 4 24988358 2.56E-06 2.56E-06
vg0402105567 sf0402101161 4 2105567 2.61E-06 2.61E-06
vg0141994613 sf0141993570 1 41994613 2.78E-06 2.78E-06
vg1218168020 sf1218139456 12 18168020 2.88E-06 2.88E-06
vg0402100710 sf0402096304 4 2100710 3.52E-06 3.52E-06
vg0100397304 sf0100396304 1 397304 3.59E-06 3.59E-06
vg0122706460 sf0122705415 1 22706460 4.18E-06 4.18E-06
vg0701530157 sf0701529157 7 1530157 4.37E-06 4.37E-06
vg0510317154 sf0510317083 5 10317154 4.74E-06 4.74E-06
vg1122446629 sf1121980500 11 22446629 4.79E-06 4.79E-06