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 mr1820 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
vg0825948249 sf0825945535 8 25948249 2.42E-07 NA
vg1127158886 sf1126687273 11 27158886 3.60E-07 2.30E-06
vg0623833223 sf0623832226 6 23833223 6.47E-07 1.67E-06
vg1110517362 sf1110511907 11 10517362 NA 2.70E-06
vg0816073881 sf0816071167 8 16073881 NA 5.47E-06