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 mr1517 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
vg0137881242 sf0137880199 1 37881242 2.33E-11 2.88E-10
vg1121710869 sf1121244746 11 21710869 4.00E-09 2.64E-08
vg1122373560 sf1121907431 11 22373560 4.09E-09 2.80E-07
vg1209876216 sf1209873626 12 9876216 9.67E-08 9.90E-09
vg0709670800 sf0709669806 7 9670800 1.44E-07 5.01E-07
vg1122427075 sf1121960946 11 22427075 3.77E-07 9.69E-07
vg0711095758 sf0711094764 7 11095758 4.12E-07 5.41E-07
vg1121694792 sf1121228669 11 21694792 5.22E-07 5.52E-06
vg0918882956 sf0918881956 9 18882956 7.11E-07 1.34E-06
vg1222234300 sf1222200847 12 22234300 1.82E-06 1.28E-06
vg0806948099 sf0806947104 8 6948099 3.25E-06 2.01E-06
vg0311072594 sf0311071312 3 11072594 8.66E-06 1.67E-07
vg1127227168 sf1126755555 11 27227168 9.10E-06 3.13E-06
vg1123222536 sf1122756407 11 23222536 NA 3.18E-06
vg0202628743 sf0202628741 2 2628743 NA 3.82E-06