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 mr1010 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
vg0305205234 sf0305204234 3 5205234 5.27E-09 NA
vg0621396998 sf0621396001 6 21396998 9.32E-09 1.18E-07
vg1218102055 sf1218073491 12 18102055 1.35E-08 NA
vg0621396414 sf0621395417 6 21396414 1.85E-08 9.55E-08
vg1000778123 sf1000777099 10 778123 6.85E-08 NA
vg1118481523 sf1118015381 11 18481523 9.96E-08 NA
vg0621415002 sf0621414005 6 21415002 2.02E-07 3.28E-07
vg0414201150 sf0414191866 4 14201150 4.40E-07 2.12E-06
vg0621266883 sf0621265886 6 21266883 8.24E-07 6.23E-07
vg0414466419 sf0414457132 4 14466419 8.55E-07 NA