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 mr1099 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
vg0222743508 sf0222737639 2 22743508 5.12E-45 5.07E-36
vg0222726032 sf0222720163 2 22726032 1.02E-44 2.00E-36
vg0222765370 sf0222759501 2 22765370 4.29E-15 5.42E-09
vg0222634177 sf0222628308 2 22634177 1.56E-11 1.00E-07
vg0222864947 sf0222859078 2 22864947 5.69E-11 7.19E-10
vg0222879623 sf0222873754 2 22879623 1.75E-10 1.97E-10
vg0224013851 sf0224007982 2 24013851 4.58E-10 1.25E-07
vg0223078170 sf0223072301 2 23078170 2.02E-09 2.72E-08
vg0224832469 sf0224826600 2 24832469 1.02E-06 7.70E-07
vg0610681687 sf0610680688 6 10681687 1.74E-06 9.89E-06
vg0223695952 sf0223690083 2 23695952 5.91E-06 2.88E-07
vg0222681985 sf0222676116 2 22681985 7.98E-06 2.29E-06
vg1115971998 sf1115506870 11 15971998 NA 4.31E-06
vg0223039697 sf0223033828 2 23039697 NA 4.67E-06