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 mr1471 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
vg0336243988 sf0336236914 3 36243988 7.67E-07 1.62E-06
vg0816220261 sf0816217547 8 16220261 8.75E-07 2.72E-06
vg0910414094 sf0910413093 9 10414094 1.47E-06 2.99E-06
vg1218022752 sf1217994188 12 18022752 2.31E-06 2.08E-06
vg1009640159 sf1009568980 10 9640159 6.95E-06 3.80E-06
vg1200812566 sf1200811566 12 812566 NA 1.37E-06
vg0526987474 sf0526924830 5 26987474 NA 3.92E-06
vg0301373348 sf0301372346 3 1373348 NA 4.04E-06