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 mr1219 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
vg0605274340 sf0605273341 6 5274340 2.09E-46 7.69E-24
vg0605299036 sf0605298037 6 5299036 1.21E-40 7.97E-21
vg0605335883 sf0605334884 6 5335883 2.56E-38 1.28E-14
vg0605219412 sf0605218413 6 5219412 4.06E-30 3.31E-11
vg0605322557 sf0605321558 6 5322557 2.78E-27 2.03E-09
vg0605316987 sf0605315988 6 5316987 7.21E-21 2.48E-06
vg0604973186 sf0604972187 6 4973186 9.99E-15 3.87E-06
vg0919681714 sf0919681304 9 19681714 4.55E-13 NA
vg0134671199 sf0134670156 1 34671199 6.48E-13 NA
vg0600826406 sf0600825407 6 826406 1.32E-12 NA
vg0605481649 sf0604784202 6 5481649 1.39E-12 5.70E-07
vg1120254935 sf1119788857 11 20254935 NA 1.74E-07
vg0605617450 sf0605616451 6 5617450 NA 1.05E-06