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 mr1137 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
vg0427390584 sf0427205448 4 27390584 3.62E-08 NA
vg0800495835 sf0800494835 8 495835 4.17E-08 NA
vg0311292417 sf0311291135 3 11292417 7.54E-08 NA
vg0911580908 sf0911579907 9 11580908 8.43E-08 3.98E-06
vg0431498650 sf0431313549 4 31498650 8.66E-08 NA
vg0119838948 sf0119837903 1 19838948 1.12E-07 NA
vg1214586572 sf1214583912 12 14586572 1.20E-06 1.96E-07