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 mr1342 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
vg1208053849 sf1208051255 12 8053849 1.09E-07 1.09E-07
vg1117477925 sf1117011780 11 17477925 1.00E-06 1.00E-06
vg0224652524 sf0224646655 2 24652524 1.43E-06 1.43E-06
vg0912289878 sf0912288877 9 12289878 3.30E-06 3.30E-06
vg0729266016 sf0729265024 7 29266016 4.17E-06 4.17E-06
vg0316396025 sf0316394670 3 16396025 7.16E-06 7.16E-06
vg0520403770 sf0520341242 5 20403770 7.54E-06 7.54E-06
vg0327847208 sf0327840262 3 27847208 8.22E-06 8.22E-06