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 mr1956 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
vg0427400029 sf0427214893 4 27400029 3.33E-07 3.33E-07
vg0518766176 sf0518703659 5 18766176 3.41E-07 3.41E-07
vg1219568312 sf1219539782 12 19568312 5.46E-07 5.44E-07
vg1219556254 sf1219527724 12 19556254 5.81E-07 5.79E-07
vg0500823853 sf0500823835 5 823853 7.74E-07 7.75E-07
vg0138861491 sf0138860448 1 38861491 9.72E-07 9.68E-07
vg0205968822 sf0205968822 2 5968822 1.39E-06 1.39E-06
vg0922539520 sf0922539039 9 22539520 2.39E-06 2.38E-06
vg0623056011 sf0623055014 6 23056011 2.61E-06 2.60E-06
vg1215726806 sf1215724103 12 15726806 3.99E-06 3.99E-06
vg1009510905 sf1009439726 10 9510905 4.19E-06 4.19E-06
vg0224129878 sf0224124009 2 24129878 4.60E-06 4.60E-06