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 mr1798 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
vg0402403542 sf0402399137 4 2403542 5.42E-10 1.33E-07
vg0402290226 sf0402285821 4 2290226 5.79E-10 1.30E-07
vg0606311325 sf0606310326 6 6311325 6.42E-08 2.94E-06
vg0718862449 sf0718861456 7 18862449 6.46E-08 NA
vg0311072594 sf0311071312 3 11072594 9.93E-07 1.04E-06
vg1222205675 sf1222172222 12 22205675 1.61E-06 1.14E-06