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 mr1717 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
vg0907445440 sf0907444440 9 7445440 1.14E-09 4.73E-07
vg0403452712 sf0403448315 4 3452712 9.71E-09 3.88E-06
vg0231595768 sf0231589899 2 31595768 1.14E-08 2.47E-07
vg0912023386 sf0912022385 9 12023386 1.22E-08 1.93E-06
vg0141730189 sf0141729146 1 41730189 3.64E-08 9.98E-06
vg0807843997 sf0807843001 8 7843997 5.39E-08 3.33E-07
vg0914534181 sf0914533180 9 14534181 1.21E-07 2.58E-07
vg0315822851 sf0315821498 3 15822851 1.04E-06 3.23E-06
vg0816930005 sf0816927291 8 16930005 2.37E-06 2.48E-06
vg0509261207 sf0509261136 5 9261207 6.40E-06 4.81E-06