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 mr1149 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
vg0222742146 sf0222736277 2 22742146 4.12E-78 6.20E-31
vg0222741535 sf0222735666 2 22741535 5.32E-78 1.03E-31
vg0601768724 sf0601767725 6 1768724 1.02E-33 NA
vg0705549134 sf0705548135 7 5549134 5.09E-33 NA
vg0604641288 sf0604640289 6 4641288 1.31E-32 NA
vg0723286803 sf0723285810 7 23286803 1.42E-32 NA
vg0600305239 sf0600304239 6 305239 1.15E-27 2.35E-06
vg0222725003 sf0222719134 2 22725003 NA 5.00E-12
vg0224382271 sf0224376402 2 24382271 NA 1.47E-08
vg0223769163 sf0223763294 2 23769163 NA 1.69E-07
vg0223506504 sf0223500635 2 23506504 NA 6.50E-07
vg0222807259 sf0222801390 2 22807259 NA 9.95E-07
vg0400147630 sf0400146630 4 147630 NA 1.03E-06
vg0224259730 sf0224253861 2 24259730 NA 1.81E-06
vg1015906056 sf1015834826 10 15906056 NA 3.55E-06
vg0223273272 sf0223267403 2 23273272 NA 4.78E-06