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 mr1133 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
vg1125501745 sf1125035584 11 25501745 1.78E-39 3.40E-20
vg0713261979 sf0713260986 7 13261979 1.27E-31 1.27E-11
vg0612546146 sf0612545147 6 12546146 1.83E-25 2.75E-10
vg0517733302 sf0517672943 5 17733302 8.41E-19 NA
vg0607912744 sf0607911745 6 7912744 1.08E-18 NA
vg1125609734 sf1125143573 11 25609734 1.38E-18 1.79E-06
vg1125876443 sf1125410362 11 25876443 2.19E-17 2.08E-06
vg1207797496 sf1207794902 12 7797496 2.21E-17 1.10E-06
vg1125611024 sf1125144863 11 25611024 4.06E-16 3.42E-07
vg0607515523 sf0607514524 6 7515523 4.35E-16 NA
vg1125520282 sf1125054121 11 25520282 2.73E-15 1.01E-06
vg1125264481 sf1124798321 11 25264481 5.34E-15 3.05E-07
vg1127723741 sf1127252127 11 27723741 NA 4.81E-08
vg1127573468 sf1127101855 11 27573468 NA 1.92E-07
vg1127186610 sf1126714997 11 27186610 NA 2.45E-07
vg1125171777 sf1124705617 11 25171777 NA 5.94E-07
vg1126298122 sf1125826535 11 26298122 NA 6.77E-07
vg1127656762 sf1127185149 11 27656762 NA 9.48E-07
vg1216368951 sf1216366247 12 16368951 NA 1.14E-06
vg1127198135 sf1126726522 11 27198135 NA 1.67E-06
vg0909301676 sf0909300675 9 9301676 NA 3.13E-06
vg1125147337 sf1124681177 11 25147337 NA 3.16E-06
vg1127387533 sf1126915920 11 27387533 NA 4.18E-06
vg0431867782 sf0431682676 4 31867782 NA 4.51E-06