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 mr1101 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
vg0222724011 sf0222718142 2 22724011 4.36E-46 6.18E-39
vg0222725905 sf0222720036 2 22725905 7.04E-46 4.63E-39
vg0222726032 sf0222720163 2 22726032 9.91E-46 6.89E-39
vg0222765370 sf0222759501 2 22765370 2.38E-15 2.73E-08
vg0222865463 sf0222859594 2 22865463 3.54E-11 1.73E-10
vg0222879623 sf0222873754 2 22879623 4.98E-11 7.25E-12
vg0222730936 sf0222725067 2 22730936 5.02E-11 1.14E-06
vg0222634177 sf0222628308 2 22634177 1.60E-10 4.31E-07
vg0224013851 sf0224007982 2 24013851 2.81E-10 3.77E-07
vg0224832469 sf0224826600 2 24832469 9.34E-08 3.20E-09
vg0223660997 sf0223655128 2 23660997 1.74E-07 9.73E-09
vg0222041029 sf0222035160 2 22041029 7.36E-07 3.41E-06
vg0218580570 sf0218574701 2 18580570 7.85E-07 1.08E-06
vg0223077958 sf0223072089 2 23077958 1.43E-06 2.55E-06
vg1112606104 sf1112142307 11 12606104 1.50E-06 6.42E-07
vg0223926615 sf0223920746 2 23926615 1.57E-06 NA
vg0224221366 sf0224215497 2 24221366 8.51E-06 1.83E-06
vg0905114178 sf0905113178 9 5114178 NA 4.71E-07
vg1212631142 sf1212628481 12 12631142 NA 1.04E-06
vg0525239875 sf0525177296 5 25239875 NA 1.09E-06
vg0223039697 sf0223033828 2 23039697 NA 1.92E-06
vg0222546189 sf0222540320 2 22546189 NA 2.84E-06
vg0610640917 sf0610639918 6 10640917 NA 3.72E-06
vg0222517140 sf0222511271 2 22517140 NA 4.69E-06
vg0610463149 sf0610462150 6 10463149 NA 4.81E-06