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 mr1213 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
vg0719039736 sf0719038743 7 19039736 2.63E-29 5.21E-22
vg0405725035 sf0405720474 4 5725035 6.36E-10 NA
vg0418469682 sf0418297727 4 18469682 6.75E-10 NA
vg0109416363 sf0109415339 1 9416363 1.01E-09 NA
vg0721979371 sf0721978378 7 21979371 1.66E-09 NA
vg0420986488 sf0420814542 4 20986488 4.36E-09 3.29E-06
vg0719053396 sf0719052403 7 19053396 NA 1.68E-06
vg0228803071 sf0228797202 2 28803071 NA 4.56E-06