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 mr1118 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
vg0421387824 sf0421215877 4 21387824 1.04E-13 4.72E-08
vg0504875404 sf0504875381 5 4875404 1.13E-11 NA
vg0434560709 sf0434375601 4 34560709 1.27E-11 NA
vg0700863821 sf0700862821 7 863821 2.66E-11 3.50E-06
vg0727970899 sf0727969906 7 27970899 2.86E-11 2.11E-06
vg1002009944 sf1002008921 10 2009944 1.04E-09 1.94E-06
vg0504952991 sf0504952969 5 4952991 1.06E-09 2.29E-06
vg1219134304 sf1219105740 12 19134304 3.73E-09 4.84E-06
vg0136191693 sf0136190650 1 36191693 4.90E-09 3.44E-06
vg1117137503 sf1116671355 11 17137503 1.89E-07 3.38E-07
vg1004500188 sf1004516726 10 4500188 2.89E-07 NA
vg1006840695 sf1006856318 10 6840695 6.62E-07 NA
vg0432345183 sf0432160072 4 32345183 8.89E-07 7.36E-08
vg0432825867 sf0432640753 4 32825867 1.36E-06 2.61E-06
vg0714435734 sf0714434741 7 14435734 NA 8.47E-07