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 mr1112 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 9.78E-43 4.18E-21
vg0610606146 sf0610605147 6 10606146 3.95E-24 1.29E-16
vg0610412049 sf0610411050 6 10412049 2.82E-22 7.28E-12
vg0610412787 sf0610411788 6 10412787 3.58E-22 4.42E-12
vg0610645680 sf0610644681 6 10645680 2.00E-18 2.72E-11
vg0610683043 sf0610682044 6 10683043 3.70E-18 4.90E-13
vg0617223679 sf0617222682 6 17223679 6.25E-17 NA
vg0610874933 sf0610873934 6 10874933 3.17E-15 4.19E-08
vg0610792001 sf0610791002 6 10792001 6.61E-14 1.15E-07
vg0610278393 sf0610277394 6 10278393 8.28E-12 2.03E-06
vg0610148252 sf0610147253 6 10148252 2.96E-11 1.19E-06
vg0617658067 sf0617657070 6 17658067 8.33E-10 3.23E-06
vg0610642043 sf0610641044 6 10642043 1.45E-09 6.96E-09
vg0611325370 sf0611324371 6 11325370 1.56E-09 1.41E-06
vg0613039521 sf0613038522 6 13039521 2.40E-09 3.40E-06
vg0611649853 sf0611648854 6 11649853 2.91E-09 6.62E-07
vg0611098102 sf0611097103 6 11098102 3.88E-09 2.92E-07
vg0226057933 sf0226052064 2 26057933 NA 4.27E-07
vg0127888116 sf0127887072 1 27888116 NA 5.38E-07
vg1017015778 sf1016944550 10 17015778 NA 1.30E-06
vg0610611540 sf0610610541 6 10611540 NA 1.63E-06
vg0206372366 sf0206372366 2 6372366 NA 2.18E-06
vg0612112236 sf0612111237 6 12112236 NA 2.77E-06
vg0616628202 sf0616627204 6 16628202 NA 3.36E-06
vg1116692719 sf1116227596 11 16692719 NA 3.68E-06
vg1214622240 sf1214619580 12 14622240 NA 4.09E-06