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 mr1069 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
vg0222742146 sf0222736277 2 22742146 3.32E-44 1.30E-27
vg0222738038 sf0222732169 2 22738038 6.59E-42 6.83E-28
vg0223769163 sf0223763294 2 23769163 3.32E-14 8.74E-09
vg0223683609 sf0223677740 2 23683609 5.87E-14 5.14E-08
vg0224640486 sf0224634617 2 24640486 4.52E-12 3.82E-06
vg0222730075 sf0222724206 2 22730075 6.76E-12 3.89E-07
vg0223556553 sf0223550684 2 23556553 1.20E-10 NA
vg0224639311 sf0224633442 2 24639311 1.69E-10 2.16E-06
vg0222656032 sf0222650163 2 22656032 2.66E-10 7.27E-10
vg0224294117 sf0224288248 2 24294117 5.66E-10 1.60E-06
vg0222041029 sf0222035160 2 22041029 5.28E-09 3.25E-06
vg1203611723 sf1203610722 12 3611723 1.40E-08 1.12E-06
vg0223077958 sf0223072089 2 23077958 1.65E-08 1.47E-06
vg0225406731 sf0225400862 2 25406731 2.67E-07 1.44E-06
vg0800669849 sf0800668849 8 669849 5.92E-07 NA
vg0809553553 sf0809552557 8 9553553 7.70E-06 4.83E-06
vg0110090809 sf0110089785 1 10090809 NA 2.90E-06