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 mr1395 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
vg0406562314 sf0406557757 4 6562314 2.57E-22 3.05E-16
vg0406519287 sf0406514730 4 6519287 4.60E-22 1.55E-16
vg0406266615 sf0406262055 4 6266615 1.94E-21 3.58E-15
vg1016565386 sf1016494159 10 16565386 3.11E-10 2.22E-06
vg0722546543 sf0722545550 7 22546543 1.47E-08 6.54E-06
vg0823019901 sf0823017188 8 23019901 2.47E-08 1.16E-06
vg0724064070 sf0724063076 7 24064070 2.62E-08 9.53E-06
vg1209921454 sf1209918864 12 9921454 3.26E-07 1.74E-06
vg0105393860 sf0105392860 1 5393860 NA 4.58E-06