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 mr1318 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
vg1215178307 sf1215175643 12 15178307 5.58E-09 NA
vg0726931180 sf0726930186 7 26931180 7.27E-09 2.70E-06
vg1104978992 sf1104974803 11 4978992 1.44E-08 3.85E-06
vg1107330232 sf1107325977 11 7330232 5.79E-08 8.00E-06
vg1210206055 sf1210203466 12 10206055 6.16E-08 NA
vg0431411704 sf0431226602 4 31411704 2.16E-07 2.01E-06
vg0823213341 sf0823210628 8 23213341 6.71E-07 2.00E-06
vg0511023890 sf0511023819 5 11023890 4.14E-06 2.23E-07
vg0131326254 sf0131325210 1 31326254 6.44E-06 NA