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 mr1757 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
vg0709269240 sf0709268246 7 9269240 1.27E-16 1.72E-07
vg1000636049 sf1000635025 10 636049 1.67E-13 6.66E-08
vg0414221572 sf0414212285 4 14221572 3.55E-13 NA
vg0404308565 sf0404304171 4 4308565 1.25E-12 9.01E-06
vg0414201150 sf0414191866 4 14201150 1.76E-12 4.58E-06
vg0505433103 sf0505433081 5 5433103 1.98E-12 NA
vg0906350119 sf0906349119 9 6350119 2.36E-11 5.16E-07
vg0402921204 sf0402916810 4 2921204 9.24E-11 1.96E-07
vg0729015054 sf0729014062 7 29015054 1.35E-10 3.97E-06
vg0416659011 sf0416487051 4 16659011 1.36E-10 7.95E-07
vg1201304030 sf1201303030 12 1304030 1.38E-10 1.22E-06
vg0602753568 sf0602752569 6 2753568 1.68E-10 1.44E-06
vg0705289004 sf0705288005 7 5289004 1.90E-10 2.71E-07
vg0209688142 sf0209688140 2 9688142 7.60E-10 4.62E-06
vg0522118727 sf0522056169 5 22118727 2.38E-09 1.78E-06
vg0140624855 sf0140623812 1 40624855 3.92E-09 NA
vg0705473234 sf0705472235 7 5473234 2.18E-08 NA
vg0621414627 sf0621413630 6 21414627 3.77E-08 2.08E-07
vg0134578272 sf0134577229 1 34578272 6.11E-08 4.12E-06
vg0619238891 sf0619237894 6 19238891 7.88E-08 NA
vg0404607481 sf0404603084 4 4607481 NA 7.02E-09
vg1202415264 sf1202414265 12 2415264 NA 2.28E-08
vg0807824555 sf0807823559 8 7824555 NA 1.12E-06
vg0204738973 sf0204738970 2 4738973 NA 3.09E-06
vg0108564628 sf0108563628 1 8564628 NA 4.42E-06
vg0621487930 sf0621486933 6 21487930 NA 6.67E-06