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 mr1199 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
vg0719042406 sf0719041413 7 19042406 2.84E-24 1.47E-09
vg0707584468 sf0707583473 7 7584468 4.88E-19 NA
vg0715259376 sf0715258383 7 15259376 5.17E-19 NA
vg1108350824 sf1108345434 11 8350824 5.18E-19 NA
vg0332576671 sf0332569542 3 32576671 7.11E-19 NA
vg0406837723 sf0406833168 4 6837723 3.05E-17 2.34E-06
vg1207833484 sf1207830890 12 7833484 NA 3.93E-08
vg0719346699 sf0719345706 7 19346699 NA 2.68E-07
vg0328058285 sf0328051339 3 28058285 NA 3.86E-06
vg1006524724 sf1006540347 10 6524724 NA 4.22E-06
vg1106572640 sf1106568393 11 6572640 NA 4.45E-06
vg1200962657 sf1200961657 12 962657 NA 4.93E-06