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 mr1176 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
vg0613340957 sf0613339958 6 13340957 1.98E-53 5.56E-17
vg0613452440 sf0613451441 6 13452440 1.97E-51 4.25E-18
vg0619710671 sf0619709674 6 19710671 2.64E-48 1.18E-10
vg0616819865 sf0616818867 6 16819865 1.22E-44 4.25E-10
vg0616847907 sf0616846909 6 16847907 3.21E-44 5.63E-12
vg0630879938 sf0630878940 6 30879938 NA 1.48E-07
vg0630882488 sf0630881490 6 30882488 NA 2.40E-07
vg0613463494 sf0613462495 6 13463494 NA 1.30E-06
vg0804351434 sf0804350437 8 4351434 NA 1.48E-06
vg1218169210 sf1218140646 12 18169210 NA 1.58E-06
vg0315341253 sf0315339900 3 15341253 NA 1.82E-06
vg0315390589 sf0315389236 3 15390589 NA 1.84E-06
vg0516238439 sf0516180921 5 16238439 NA 2.29E-06
vg1218169348 sf1218140784 12 18169348 NA 3.39E-06