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 mr1462 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
vg0101329001 sf0101328001 1 1329001 3.43E-07 3.43E-07
vg0324094127 sf0324092206 3 24094127 3.55E-07 3.55E-07
vg0101329012 sf0101328012 1 1329012 3.85E-07 3.84E-07
vg0224875540 sf0224869671 2 24875540 5.15E-07 5.16E-07
vg1218064708 sf1218036144 12 18064708 3.13E-06 3.12E-06
vg0421264360 sf0421092413 4 21264360 3.54E-06 3.54E-06
vg0308714978 sf0308713916 3 8714978 4.85E-06 4.83E-06