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 mr1842 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
vg0331273085 sf0331265970 3 31273085 9.14E-35 2.54E-18
vg0330601042 sf0330593931 3 30601042 1.16E-14 6.79E-07
vg0330602937 sf0330595826 3 30602937 5.41E-14 4.36E-07
vg0205108560 sf0205108557 2 5108560 7.20E-14 NA
vg0204862895 sf0204862892 2 4862895 1.12E-12 NA
vg0331770573 sf0331763450 3 31770573 1.20E-11 7.18E-06
vg0331359176 sf0331352061 3 31359176 7.21E-10 6.91E-09
vg0906303350 sf0906302350 9 6303350 1.87E-08 5.65E-06
vg0306413930 sf0306412930 3 6413930 9.08E-08 NA
vg0304654587 sf0304653589 3 4654587 2.88E-07 NA
vg1216545702 sf1216542995 12 16545702 7.11E-07 NA
vg0117142011 sf0117140965 1 17142011 NA 2.71E-06
vg0319782833 sf0319781344 3 19782833 NA 4.12E-06