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 mr1677 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
vg0316269128 sf0316267775 3 16269128 1.66E-08 NA
vg0430628468 sf0430443343 4 30628468 2.84E-08 NA
vg0607815296 sf0607814297 6 7815296 3.19E-08 NA
vg0234397577 sf0234391708 2 34397577 3.56E-08 NA
vg0701536569 sf0701535569 7 1536569 3.66E-08 NA
vg0416033751 sf0415861784 4 16033751 3.12E-07 7.37E-06
vg0230050221 sf0230044352 2 30050221 3.46E-07 NA
vg0228468795 sf0228462926 2 28468795 2.08E-06 NA
vg0226817643 sf0226811774 2 26817643 2.27E-06 NA
vg0816444910 sf0816442196 8 16444910 NA 7.58E-07