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 mr1107 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 1.23E-33 7.28E-23
vg0719270235 sf0719269242 7 19270235 6.63E-19 1.23E-08
vg0719317820 sf0719316827 7 19317820 1.50E-17 5.27E-09
vg0717192350 sf0717191357 7 17192350 1.87E-17 1.47E-11
vg1201654412 sf1201653412 12 1654412 5.86E-17 3.81E-10
vg0719242312 sf0719241319 7 19242312 4.14E-16 3.14E-08
vg0719250400 sf0719249407 7 19250400 5.48E-16 2.56E-08
vg0719153233 sf0719152240 7 19153233 1.54E-13 5.25E-07
vg0719131795 sf0719130802 7 19131795 4.19E-12 1.72E-06
vg0228211032 sf0228205163 2 28211032 5.81E-12 2.57E-07
vg0611537596 sf0611536597 6 11537596 7.80E-12 8.62E-07
vg0719465974 sf0719464981 7 19465974 9.55E-12 4.34E-09
vg0719527910 sf0719526917 7 19527910 8.34E-11 2.04E-06
vg0706878861 sf0706877866 7 6878861 1.54E-10 1.90E-06
vg0612290452 sf0612289453 6 12290452 8.91E-10 1.01E-08
vg0307861794 sf0307860732 3 7861794 2.89E-08 1.04E-06
vg0717334017 sf0717333024 7 17334017 5.02E-08 1.88E-07
vg0718985437 sf0718984444 7 18985437 8.96E-08 2.27E-08
vg0504291251 sf0504291228 5 4291251 2.56E-07 7.43E-07
vg1214370012 sf1214367353 12 14370012 7.08E-07 NA
vg0619448815 sf0619447818 6 19448815 1.74E-06 NA
vg0401200371 sf0401195921 4 1200371 3.54E-06 NA
vg0501722287 sf0501722271 5 1722287 5.97E-06 NA
vg0507595464 sf0507595405 5 7595464 NA 3.12E-07
vg0211829965 sf0211829961 2 11829965 NA 9.58E-07
vg0336362940 sf0336355810 3 36362940 NA 1.18E-06