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 mr1539 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
vg0132648983 sf0132647939 1 32648983 2.57E-19 NA
vg1216157169 sf1216154465 12 16157169 1.06E-18 8.45E-06
vg0232156909 sf0232151040 2 32156909 1.56E-18 NA
vg0130052727 sf0130051682 1 30052727 3.49E-18 NA
vg1125434956 sf1124968795 11 25434956 3.59E-18 NA
vg1016117610 sf1016046382 10 16117610 7.86E-18 4.20E-06
vg0129887798 sf0129886753 1 29887798 1.45E-17 9.32E-06
vg0817500434 sf0817497720 8 17500434 NA 8.09E-07
vg0910099182 sf0910098181 9 10099182 NA 1.07E-06
vg0905283103 sf0905282103 9 5283103 NA 1.88E-06
vg0129761733 sf0129760688 1 29761733 NA 4.73E-06
vg1120481051 sf1120014976 11 20481051 NA 6.01E-06