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 mr1458 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
vg1218526277 sf1218497713 12 18526277 1.99E-80 2.00E-17
vg1218514358 sf1218485794 12 18514358 4.15E-78 2.76E-19
vg1218704787 sf1218676222 12 18704787 6.94E-74 4.31E-15
vg0141109776 sf0141108733 1 41109776 1.71E-54 NA
vg0627836229 sf0627835231 6 27836229 1.77E-54 NA
vg1204491827 sf1204490815 12 4491827 1.57E-52 NA
vg0425130701 sf0424945562 4 25130701 9.04E-52 NA
vg1218493508 sf1218464944 12 18493508 NA 1.48E-09
vg1218448864 sf1218420300 12 18448864 NA 6.94E-09
vg0406750129 sf0406745575 4 6750129 NA 8.01E-09
vg0200452314 sf0200452314 2 452314 NA 9.31E-08
vg1218328298 sf1218299734 12 18328298 NA 1.56E-07
vg1218850297 sf1218821732 12 18850297 NA 5.36E-07
vg0922613922 sf0922613441 9 22613922 NA 1.07E-06
vg1218591659 sf1218563095 12 18591659 NA 1.27E-06
vg0812252841 sf0812251846 8 12252841 NA 1.70E-06
vg1219406217 sf1219377687 12 19406217 NA 3.55E-06
vg1218883751 sf1218855186 12 18883751 NA 3.62E-06
vg0827226611 sf0827223897 8 27226611 NA 3.71E-06
vg0827225803 sf0827223089 8 27225803 NA 4.31E-06
vg0141000513 sf0140999470 1 41000513 NA 4.79E-06