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 mr1466 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
vg1210647989 sf1210645402 12 10647989 7.77E-08 NA
vg0915815139 sf0915814138 9 15815139 9.77E-07 1.26E-06
vg0920181836 sf0920181355 9 20181836 5.10E-06 NA
vg0918774898 sf0918773898 9 18774898 9.84E-06 3.71E-06
vg0916030541 sf0916029540 9 16030541 NA 2.69E-06
vg0203000556 sf0203000554 2 3000556 NA 6.08E-06