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 mr1873 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
vg0506869268 sf0506869210 5 6869268 8.21E-12 1.37E-07
vg0506837520 sf0506837462 5 6837520 9.13E-12 1.72E-09
vg0506898674 sf0506898616 5 6898674 5.34E-11 1.48E-09
vg0514682946 sf0514625489 5 14682946 1.45E-09 5.45E-09
vg0514648404 sf0514590947 5 14648404 5.52E-09 1.97E-09
vg0427858776 sf0427673638 4 27858776 5.67E-09 2.03E-06
vg0431894928 sf0431709823 4 31894928 9.17E-09 3.27E-06
vg0427867420 sf0427682282 4 27867420 1.65E-08 5.81E-07
vg0500197693 sf0500197693 5 197693 4.66E-08 4.61E-06
vg1107375253 sf1107370998 11 7375253 1.01E-06 5.43E-07
vg0117519898 sf0117518852 1 17519898 1.29E-06 2.30E-06
vg0500124999 sf0500124999 5 124999 8.65E-06 NA
vg0624726893 sf0624725896 6 24726893 NA 1.68E-07