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 mr1554 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
vg0716931835 sf0716930842 7 16931835 1.90E-12 1.04E-06
vg0821752459 sf0821749746 8 21752459 2.40E-11 NA
vg0920759077 sf0920758596 9 20759077 3.02E-11 NA
vg0518737276 sf0518674759 5 18737276 3.04E-11 NA
vg0523508245 sf0523445666 5 23508245 3.61E-11 NA
vg0420889762 sf0420717805 4 20889762 2.39E-09 4.40E-06
vg1204019821 sf1204018809 12 4019821 7.16E-09 NA
vg0627002372 sf0627001375 6 27002372 1.11E-08 2.80E-06
vg0603907011 sf0603906012 6 3907011 8.01E-08 5.17E-06
vg0627586702 sf0627585704 6 27586702 NA 1.57E-06
vg0826935533 sf0826932819 8 26935533 NA 2.40E-06
vg0905608023 sf0905607023 9 5608023 NA 3.36E-06
vg0723177719 sf0723176726 7 23177719 NA 4.56E-06