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 mr1092 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
vg0130670983 sf0130669939 1 30670983 3.09E-19 1.18E-15
vg0136174549 sf0136173506 1 36174549 2.21E-08 NA
vg1200436988 sf1200435988 12 436988 2.23E-08 NA
vg1203606223 sf1203605222 12 3606223 3.19E-08 NA
vg0140047043 sf0140046000 1 40047043 4.25E-08 5.27E-06
vg0528474996 sf0528412351 5 28474996 1.86E-07 1.33E-06
vg0139919512 sf0139918469 1 39919512 6.39E-07 1.32E-06
vg0129955088 sf0129954043 1 29955088 NA 3.67E-07
vg0130861999 sf0130860955 1 30861999 NA 1.82E-06