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 mr1624 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
vg0433627526 sf0433442409 4 33627526 2.45E-10 NA
vg0920313066 sf0920312585 9 20313066 1.27E-08 NA
vg0300230399 sf0300229399 3 230399 2.70E-08 NA
vg1002299754 sf1002298731 10 2299754 3.95E-08 NA
vg1116955967 sf1116490844 11 16955967 4.35E-08 NA
vg1022686258 sf1022614732 10 22686258 1.41E-07 5.39E-07
vg1212172403 sf1212169740 12 12172403 2.01E-07 4.09E-06
vg0916352151 sf0916351150 9 16352151 2.64E-07 4.92E-06
vg0413192353 sf0413183063 4 13192353 3.19E-07 NA
vg1207616892 sf1207614298 12 7616892 3.25E-07 4.91E-06
vg1215272298 sf1215269596 12 15272298 4.00E-06 7.55E-06
vg1111322133 sf1111316450 11 11322133 NA 4.22E-06