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 mr1011 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
vg0434000706 sf0433815599 4 34000706 5.96E-17 3.43E-09
vg0433925642 sf0433740539 4 33925642 6.70E-17 1.23E-09
vg0122505956 sf0122504911 1 22505956 7.61E-16 2.49E-07
vg1207987250 sf1207984656 12 7987250 1.31E-15 2.33E-06
vg0428421211 sf0428236065 4 28421211 2.70E-15 1.50E-07
vg0410594507 sf0410585206 4 10594507 2.33E-14 NA
vg1207916494 sf1207913900 12 7916494 1.49E-13 NA
vg1208320508 sf1208317914 12 8320508 9.85E-13 6.96E-07
vg0416328791 sf0416156824 4 16328791 NA 6.04E-07
vg0134092893 sf0134091849 1 34092893 NA 9.23E-07
vg0302286989 sf0302285985 3 2286989 NA 2.51E-06
vg0725369051 sf0725368057 7 25369051 NA 4.56E-06
vg0726119227 sf0726118233 7 26119227 NA 7.52E-06