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 mr1604 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
vg0918774898 sf0918773898 9 18774898 1.02E-08 1.02E-08
vg0805095019 sf0805094022 8 5095019 2.51E-07 2.51E-07
vg0314986971 sf0314985618 3 14986971 3.07E-07 3.07E-07
vg0223170170 sf0223164301 2 23170170 5.49E-07 5.49E-07
vg0915815139 sf0915814138 9 15815139 7.87E-07 7.88E-07
vg0223074046 sf0223068177 2 23074046 8.11E-07 8.12E-07
vg0207698155 sf0207698154 2 7698155 1.33E-06 1.33E-06
vg1014073653 sf1014002419 10 14073653 1.65E-06 1.65E-06
vg0400149978 sf0400148978 4 149978 2.08E-06 2.08E-06
vg0906624349 sf0906623349 9 6624349 3.75E-06 3.75E-06
vg1213717963 sf1213715301 12 13717963 3.95E-06 3.95E-06