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 mr1878 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
vg0719001862 sf0719000869 7 19001862 9.00E-20 2.82E-16
vg0717192350 sf0717191357 7 17192350 1.75E-11 3.87E-09
vg0719270235 sf0719269242 7 19270235 6.61E-11 2.42E-07
vg0613011415 sf0613010416 6 13011415 4.05E-10 1.50E-07
vg0719449907 sf0719448914 7 19449907 4.90E-10 6.97E-08
vg1201356688 sf1201355688 12 1356688 8.79E-10 2.62E-06
vg0401153559 sf0401149109 4 1153559 6.78E-09 1.63E-08
vg0719135311 sf0719134318 7 19135311 1.08E-08 4.90E-06
vg0401152900 sf0401148450 4 1152900 1.37E-08 3.78E-08
vg0401155869 sf0401151419 4 1155869 1.67E-08 3.91E-07
vg1207833484 sf1207830890 12 7833484 5.38E-08 6.96E-08
vg0235249589 sf0235243720 2 35249589 9.37E-08 6.65E-07
vg0407629615 sf0407624882 4 7629615 1.29E-06 NA
vg0717315974 sf0717314981 7 17315974 2.92E-06 1.58E-06
vg0718985437 sf0718984444 7 18985437 6.86E-06 5.21E-07
vg0716091815 sf0716090822 7 16091815 NA 4.94E-06