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 mr1210 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
vg1005695540 sf1005712078 10 5695540 9.17E-39 6.15E-12
vg1010636917 sf1010565738 10 10636917 6.48E-32 2.43E-08
vg0434705432 sf0434520321 4 34705432 5.10E-31 1.30E-06
vg0327159737 sf0327152790 3 27159737 2.04E-29 NA
vg1209356739 sf1209354148 12 9356739 3.92E-28 NA
vg0335000939 sf0334993809 3 35000939 9.87E-25 4.93E-07
vg0327425445 sf0327418498 3 27425445 1.11E-22 1.24E-15
vg0327447631 sf0327440684 3 27447631 NA 1.77E-14
vg0317023117 sf0317021991 3 17023117 NA 9.51E-14
vg1005967804 sf1005984342 10 5967804 NA 2.27E-12
vg0202735231 sf0202735229 2 2735231 NA 1.02E-11
vg0324795678 sf0324793757 3 24795678 NA 2.84E-11
vg0628049712 sf0628048714 6 28049712 NA 1.31E-10
vg0222830353 sf0222824484 2 22830353 NA 8.19E-10
vg0220269450 sf0220263582 2 20269450 NA 1.70E-09
vg0304861604 sf0304860606 3 4861604 NA 2.82E-09
vg0400407662 sf0400406660 4 407662 NA 3.12E-09
vg0605613230 sf0605612231 6 5613230 NA 5.36E-09
vg1005691507 sf1005708045 10 5691507 NA 5.86E-09
vg0907825976 sf0907824976 9 7825976 NA 8.96E-09
vg0628001136 sf0628000138 6 28001136 NA 9.21E-09
vg0222778846 sf0222772977 2 22778846 NA 1.16E-08
vg1004952643 sf1004969180 10 4952643 NA 2.30E-08
vg0430570531 sf0430385406 4 30570531 NA 2.93E-08
vg1110517362 sf1110511907 11 10517362 NA 1.06E-07