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 mr1235 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
vg0216991508 sf0216985638 2 16991508 1.59E-61 6.26E-14
vg0216623044 sf0216617174 2 16623044 3.69E-60 5.71E-15
vg0216838688 sf0216832818 2 16838688 2.77E-59 5.55E-15
vg0216822884 sf0216817014 2 16822884 3.30E-55 8.19E-24
vg0718770788 sf0718769795 7 18770788 5.93E-46 NA
vg0310434982 sf0310433898 3 10434982 3.35E-45 NA
vg0619310650 sf0619309653 6 19310650 1.65E-44 NA
vg0217137734 sf0217131864 2 17137734 NA 1.77E-12
vg0812023942 sf0812022947 8 12023942 NA 1.21E-08
vg0212179963 sf0212179959 2 12179963 NA 1.85E-08
vg0713784416 sf0713783423 7 13784416 NA 1.13E-07
vg0216574324 sf0216568454 2 16574324 NA 1.26E-07
vg1114473442 sf1114009759 11 14473442 NA 7.71E-07
vg0216773376 sf0216767506 2 16773376 NA 1.09E-06
vg0813447304 sf0813444857 8 13447304 NA 3.61E-06