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 mr1784 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
vg1019088726 sf1019017283 10 19088726 4.21E-58 2.90E-10
vg1019101727 sf1019030284 10 19101727 1.30E-57 1.23E-10
vg0204368620 sf0204368617 2 4368620 5.93E-50 NA
vg1224594467 sf1224560921 12 24594467 6.12E-50 NA
vg0106176553 sf0106175553 1 6176553 3.94E-48 NA
vg0132621629 sf0132620585 1 32621629 5.19E-48 NA
vg0432523363 sf0432338255 4 32523363 NA 7.06E-10
vg0432592187 sf0432407078 4 32592187 NA 1.01E-07
vg0432594893 sf0432409784 4 32594893 NA 3.01E-07
vg1018583195 sf1018511752 10 18583195 NA 3.64E-07
vg0434575713 sf0434390605 4 34575713 NA 4.36E-07
vg0132607031 sf0132605987 1 32607031 NA 2.21E-06
vg1004059501 sf1004058477 10 4059501 NA 2.24E-06
vg0400503363 sf0400502361 4 503363 NA 2.69E-06
vg0826228501 sf0826225787 8 26228501 NA 3.58E-06
vg0815289622 sf0815286908 8 15289622 NA 3.89E-06
vg1006456919 sf1006472542 10 6456919 NA 4.82E-06
vg0317957936 sf0317956718 3 17957936 NA 4.86E-06
vg0821199166 sf0821196453 8 21199166 NA 5.94E-06