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 mr1722 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
vg0402663053 sf0402658657 4 2663053 1.62E-07 1.62E-07
vg0919811754 sf0919811273 9 19811754 6.72E-07 6.73E-07
vg1218050442 sf1218021878 12 18050442 7.82E-07 7.82E-07
vg0101001636 sf0101000636 1 1001636 1.14E-06 1.14E-06
vg1126525051 sf1126053466 11 26525051 3.07E-06 3.07E-06
vg0318510912 sf0318509694 3 18510912 3.25E-06 3.25E-06
vg0122730523 sf0122729479 1 22730523 4.07E-06 4.07E-06