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 mr1406 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
vg0429988139 sf0429803006 4 29988139 1.99E-11 4.11E-09
vg0430327954 sf0430142828 4 30327954 5.80E-08 NA
vg1208858063 sf1208855471 12 8858063 8.62E-06 2.93E-06
vg0813416008 sf0813413561 8 13416008 NA 8.18E-07
vg0224143127 sf0224137258 2 24143127 NA 3.13E-06