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 mr1861 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
vg0300180852 sf0300179852 3 180852 1.40E-08 1.40E-08
vg0618381087 sf0618380090 6 18381087 3.00E-08 3.00E-08
vg0432345183 sf0432160072 4 32345183 6.10E-08 6.10E-08
vg0124176064 sf0124175020 1 24176064 1.18E-07 1.18E-07
vg1002920436 sf1002919413 10 2920436 1.46E-07 1.46E-07
vg0603982828 sf0603981829 6 3982828 3.18E-07 3.18E-07
vg0202460448 sf0202460446 2 2460448 5.87E-07 5.87E-07
vg1222433268 sf1222399707 12 22433268 6.69E-07 6.69E-07
vg0820847697 sf0820844984 8 20847697 7.76E-07 7.77E-07
vg1224514466 sf1224480920 12 24514466 7.93E-07 7.93E-07
vg0220941584 sf0220935716 2 20941584 9.68E-07 9.68E-07
vg1226169508 sf1226135902 12 26169508 1.10E-06 1.10E-06
vg1224010698 sf1223977151 12 24010698 1.62E-06 1.62E-06
vg0217546819 sf0217540949 2 17546819 1.81E-06 1.81E-06
vg0220734090 sf0220728222 2 20734090 1.91E-06 1.91E-06
vg0704766590 sf0704765591 7 4766590 2.69E-06 2.69E-06
vg0311437556 sf0311436274 3 11437556 3.41E-06 3.41E-06
vg0404159263 sf0404154870 4 4159263 3.69E-06 3.69E-06
vg0719707311 sf0719706318 7 19707311 4.30E-06 4.30E-06