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 mr1933 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
vg0331273085 sf0331265970 3 31273085 3.86E-25 2.26E-14
vg0222747179 sf0222741310 2 22747179 8.02E-14 4.02E-11
vg0222746191 sf0222740322 2 22746191 1.28E-13 4.05E-11
vg0222737968 sf0222732099 2 22737968 4.11E-13 2.48E-11
vg0528532728 sf0528470083 5 28532728 9.00E-12 NA
vg0208884016 sf0208884014 2 8884016 3.78E-11 NA
vg1117213282 sf1116747133 11 17213282 5.77E-11 NA
vg0331359176 sf0331352061 3 31359176 6.52E-08 2.13E-08
vg1126856638 sf1126385025 11 26856638 1.37E-07 1.07E-07
vg1002941120 sf1002940097 10 2941120 3.34E-07 4.14E-06
vg0117142011 sf0117140965 1 17142011 NA 4.09E-07
vg1005025105 sf1005041642 10 5025105 NA 7.62E-07
vg1126991344 sf1126519731 11 26991344 NA 1.04E-06
vg1128853223 sf1128330002 11 28853223 NA 4.13E-06
vg0606938203 sf0606937204 6 6938203 NA 4.61E-06