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 mr1544 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
vg0528836237 sf0528773592 5 28836237 1.78E-09 2.08E-06
vg0141892492 sf0141891449 1 41892492 4.04E-09 NA
vg0141835378 sf0141834335 1 41835378 1.59E-08 4.53E-06
vg0432564131 sf0432379022 4 32564131 4.06E-08 NA
vg0107316629 sf0107315629 1 7316629 6.35E-08 NA
vg0416255837 sf0416083870 4 16255837 7.66E-08 NA
vg0141838999 sf0141837956 1 41838999 1.67E-07 NA
vg1209241813 sf1209239222 12 9241813 NA 1.81E-06
vg0517583079 sf0517522722 5 17583079 NA 3.66E-06
vg0517981167 sf0517920653 5 17981167 NA 6.18E-06