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 mr1233 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
vg0719090536 sf0719089543 7 19090536 1.37E-18 1.97E-18
vg0718989547 sf0718988554 7 18989547 1.40E-18 5.16E-19
vg0336302800 sf0336295670 3 36302800 1.25E-12 1.33E-10
vg0719133785 sf0719132792 7 19133785 1.06E-10 1.26E-08
vg1202102394 sf1202101392 12 2102394 2.04E-09 7.70E-07
vg0719041118 sf0719040125 7 19041118 2.69E-09 9.18E-08
vg0719075935 sf0719074942 7 19075935 3.53E-09 7.45E-07
vg0305124832 sf0305123834 3 5124832 1.72E-08 1.64E-06
vg0315229088 sf0315227735 3 15229088 3.82E-08 1.38E-06
vg0335364463 sf0335357332 3 35364463 1.82E-07 5.38E-07
vg0304891426 sf0304890428 3 4891426 1.19E-06 NA
vg0224909167 sf0224903298 2 24909167 1.56E-06 NA
vg0315854657 sf0315853304 3 15854657 3.24E-06 NA
vg0628133558 sf0628132560 6 28133558 4.97E-06 1.89E-06
vg0718985954 sf0718984961 7 18985954 9.24E-06 1.03E-10
vg0713016602 sf0713015609 7 13016602 NA 3.74E-06