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 mr1091 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
vg0610559165 sf0610558166 6 10559165 1.07E-57 1.41E-30
vg0610566237 sf0610565238 6 10566237 1.45E-49 7.23E-31
vg0610680325 sf0610679326 6 10680325 1.59E-49 8.88E-27
vg0610774978 sf0610773979 6 10774978 2.10E-28 7.53E-17
vg0617223679 sf0617222682 6 17223679 6.63E-28 5.50E-09
vg0610412787 sf0610411788 6 10412787 6.12E-27 3.31E-16
vg0617383481 sf0617382484 6 17383481 2.13E-26 5.35E-09
vg0609891803 sf0609890804 6 9891803 1.63E-25 1.70E-12
vg0611887719 sf0611886720 6 11887719 2.14E-25 2.57E-12
vg0614652165 sf0614651166 6 14652165 5.14E-25 2.70E-06
vg0610556004 sf0610555005 6 10556004 5.83E-24 4.02E-15
vg0610683043 sf0610682044 6 10683043 1.99E-19 3.34E-15
vg0610643072 sf0610642073 6 10643072 1.44E-15 4.34E-11
vg0614821165 sf0614820166 6 14821165 3.74E-15 1.78E-07
vg0610444948 sf0610443949 6 10444948 7.39E-15 8.76E-08
vg0610742085 sf0610741086 6 10742085 6.92E-13 1.75E-07
vg0610679932 sf0610678933 6 10679932 1.13E-12 9.15E-14
vg0611098317 sf0611097318 6 11098317 1.42E-12 8.19E-10
vg0611002115 sf0611001116 6 11002115 1.76E-11 1.26E-07
vg0612044618 sf0612043619 6 12044618 7.29E-11 1.13E-07
vg0617807141 sf0617806144 6 17807141 3.14E-10 5.09E-07
vg0611330297 sf0611329298 6 11330297 5.01E-10 1.12E-07
vg0610442142 sf0610441143 6 10442142 7.05E-10 7.79E-08
vg0616628202 sf0616627204 6 16628202 NA 3.36E-07
vg1218724628 sf1218696063 12 18724628 NA 3.85E-07
vg0611255073 sf0611254074 6 11255073 NA 1.14E-06