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 mr1830 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
vg0411404313 sf0411395016 4 11404313 1.89E-21 9.01E-09
vg0407554949 sf0407550218 4 7554949 2.53E-19 2.30E-06
vg0414021996 sf0414012711 4 14021996 3.04E-18 NA
vg0614459942 sf0614458943 6 14459942 4.76E-16 NA
vg0905314628 sf0905313628 9 5314628 5.18E-16 NA
vg0805968808 sf0805967811 8 5968808 3.00E-13 2.74E-07
vg0821751104 sf0821748391 8 21751104 3.64E-13 NA
vg0819556794 sf0819554081 8 19556794 3.79E-11 NA
vg0805944930 sf0805943933 8 5944930 NA 7.73E-08
vg0410847838 sf0410838539 4 10847838 NA 8.50E-08
vg0407132799 sf0407128069 4 7132799 NA 2.84E-07
vg1208634025 sf1208631432 12 8634025 NA 6.57E-07
vg0913502351 sf0913501350 9 13502351 NA 2.36E-06