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 mr1229 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
vg0715576538 sf0715575545 7 15576538 8.31E-12 NA
vg0402283132 sf0402278727 4 2283132 3.53E-11 NA
vg1001244211 sf1001243188 10 1244211 3.87E-11 NA
vg0518114154 sf0518053640 5 18114154 1.17E-10 NA
vg0623363687 sf0623362690 6 23363687 1.55E-10 NA
vg0823044673 sf0823041960 8 23044673 4.53E-10 5.91E-07
vg0901360162 sf0901359162 9 1360162 5.09E-10 1.80E-07
vg1016847414 sf1016776186 10 16847414 7.83E-09 8.89E-07
vg1117596580 sf1117130437 11 17596580 1.51E-08 NA
vg1209678228 sf1209675637 12 9678228 3.79E-07 4.99E-06
vg1013275525 sf1013204295 10 13275525 1.89E-06 2.95E-06
vg0817358920 sf0817356206 8 17358920 2.43E-06 NA
vg1216321310 sf1216318606 12 16321310 NA 1.95E-06
vg0321809157 sf0321807667 3 21809157 NA 2.14E-06
vg0617039640 sf0617038643 6 17039640 NA 2.38E-06