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 mr1155 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
vg0719050935 sf0719049942 7 19050935 7.12E-13 3.01E-11
vg0422260209 sf0422075091 4 22260209 2.64E-09 7.69E-08
vg0417659454 sf0417487495 4 17659454 1.67E-08 9.54E-07
vg0417524720 sf0417352762 4 17524720 2.90E-08 7.20E-07
vg0401947660 sf0401943256 4 1947660 5.39E-08 2.11E-06
vg0721979371 sf0721978378 7 21979371 9.65E-08 3.61E-06
vg0227635783 sf0227629914 2 27635783 1.47E-07 4.77E-06
vg0901023936 sf0901022936 9 1023936 2.46E-07 4.27E-06
vg0719047994 sf0719047001 7 19047994 1.44E-06 1.53E-09
vg1213429246 sf1213426584 12 13429246 NA 4.58E-07
vg0714207090 sf0714206097 7 14207090 NA 4.30E-06