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 mr1003 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
vg0133208220 sf0133207176 1 33208220 3.97E-30 4.12E-11
vg0801556836 sf0801555838 8 1556836 5.58E-26 NA
vg0130119010 sf0130117965 1 30119010 1.56E-25 NA
vg0710364263 sf0710363269 7 10364263 1.87E-25 NA
vg0717363121 sf0717362128 7 17363121 4.14E-25 2.28E-06
vg0921431410 sf0921430929 9 21431410 4.87E-22 5.65E-08
vg0921543752 sf0921543271 9 21543752 NA 3.72E-10
vg0921420005 sf0921419524 9 21420005 NA 6.96E-10
vg0921450059 sf0921449578 9 21450059 NA 1.01E-09
vg0328947425 sf0328940477 3 28947425 NA 1.39E-07
vg0215099729 sf0215093859 2 15099729 NA 1.61E-07
vg1215956020 sf1215953316 12 15956020 NA 1.22E-06
vg1105604948 sf1105600700 11 5604948 NA 1.85E-06
vg1216261222 sf1216258518 12 16261222 NA 2.26E-06
vg1105605348 sf1105601100 11 5605348 NA 2.43E-06
vg0431857957 sf0431672851 4 31857957 NA 2.61E-06
vg0137799491 sf0137798448 1 37799491 NA 4.15E-06
vg0431831099 sf0431645992 4 31831099 NA 6.37E-06
vg0616941958 sf0616940961 6 16941958 NA 7.82E-06