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 mr1536 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
vg0921462199 sf0921461718 9 21462199 8.87E-18 1.06E-10
vg0921419848 sf0921419367 9 21419848 2.22E-14 5.93E-11
vg0611987652 sf0611986653 6 11987652 2.12E-09 NA
vg0825755939 sf0825753225 8 25755939 6.34E-09 NA
vg0335754446 sf0335747315 3 35754446 1.52E-08 NA
vg0916509097 sf0916508096 9 16509097 1.55E-08 NA
vg0401162955 sf0401158505 4 1162955 6.05E-06 NA
vg0800504571 sf0800503571 8 504571 NA 3.11E-06
vg0907264200 sf0907263200 9 7264200 NA 3.76E-06