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 mr1877 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 7.11E-22 1.62E-12
vg0610661343 sf0610660344 6 10661343 7.55E-21 1.60E-15
vg0222628680 sf0222622811 2 22628680 4.60E-17 4.22E-10
vg0617223679 sf0617222682 6 17223679 2.92E-15 1.04E-06
vg0619248810 sf0619247813 6 19248810 1.13E-14 NA
vg0612211443 sf0612210444 6 12211443 1.59E-14 NA
vg0613702743 sf0613701744 6 13702743 5.22E-14 4.70E-07
vg0222725103 sf0222719234 2 22725103 5.97E-14 1.96E-12
vg0610285087 sf0610284088 6 10285087 1.73E-13 2.87E-09
vg0421627867 sf0421455917 4 21627867 1.03E-11 8.35E-07
vg0610649149 sf0610648150 6 10649149 3.80E-11 6.32E-08
vg0222897004 sf0222891135 2 22897004 1.11E-10 2.27E-07
vg0610974808 sf0610973809 6 10974808 1.65E-10 6.25E-07
vg0414793750 sf0414784464 4 14793750 1.78E-09 2.22E-06
vg0610467785 sf0610466786 6 10467785 4.85E-09 3.10E-06
vg0610476181 sf0610475182 6 10476181 4.89E-09 2.18E-06
vg0220569457 sf0220563589 2 20569457 7.14E-08 1.22E-06
vg0414331250 sf0414321963 4 14331250 1.14E-07 NA