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 mr1362 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
vg0817612440 sf0817609727 8 17612440 2.35E-18 3.19E-06
vg0407691066 sf0407686333 4 7691066 3.90E-16 NA
vg0420455986 sf0420284030 4 20455986 5.02E-16 NA
vg0826764899 sf0826762185 8 26764899 1.11E-15 NA
vg0432685574 sf0432500463 4 32685574 1.13E-15 NA
vg1207170889 sf1207168279 12 7170889 3.03E-15 3.61E-06
vg0702732529 sf0702731530 7 2732529 1.51E-13 1.27E-06
vg0430367665 sf0430182542 4 30367665 NA 3.05E-07
vg1013275525 sf1013204295 10 13275525 NA 1.42E-06
vg0609793222 sf0609792223 6 9793222 NA 1.51E-06
vg1204993459 sf1204992445 12 4993459 NA 2.18E-06
vg0129101290 sf0129100245 1 29101290 NA 2.99E-06
vg0320217493 sf0320216004 3 20217493 NA 3.87E-06
vg0817662622 sf0817659909 8 17662622 NA 4.19E-06