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 mr1355 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
vg1003299582 sf1003298559 10 3299582 1.90E-06 1.90E-06
vg1105536393 sf1105532145 11 5536393 2.87E-06 2.87E-06
vg0909870169 sf0909869168 9 9870169 3.06E-06 3.06E-06
vg0103479251 sf0103478251 1 3479251 3.26E-06 3.26E-06
vg1105536370 sf1105532122 11 5536370 3.54E-06 3.54E-06
vg0910261090 sf0910260089 9 10261090 3.55E-06 3.55E-06
vg1225574338 sf1225540733 12 25574338 3.65E-06 3.65E-06
vg1209716053 sf1209713462 12 9716053 4.06E-06 4.06E-06
vg0410076881 sf0410067579 4 10076881 4.94E-06 4.93E-06