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 mr1437 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
vg0719049384 sf0719048391 7 19049384 5.01E-19 8.53E-16
vg0719056561 sf0719055568 7 19056561 4.06E-18 2.04E-17
vg0721979371 sf0721978378 7 21979371 1.27E-08 6.13E-06
vg0719125702 sf0719124709 7 19125702 1.67E-08 3.35E-10
vg0230814769 sf0230808900 2 30814769 4.19E-08 NA
vg0622427365 sf0622426368 6 22427365 6.75E-08 3.03E-06
vg0312684585 sf0312683303 3 12684585 1.10E-07 2.67E-06
vg0909917394 sf0909916393 9 9917394 NA 1.97E-06
vg0516162890 sf0516105374 5 16162890 NA 3.84E-06
vg1217240367 sf1217234322 12 17240367 NA 4.75E-06