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 mr1552 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
vg0312028396 sf0312027114 3 12028396 3.21E-13 8.45E-07
vg0512814053 sf0512756975 5 12814053 3.48E-13 2.25E-06
vg0912250614 sf0912249613 9 12250614 9.55E-12 NA
vg0518737276 sf0518674759 5 18737276 1.09E-11 NA
vg0412131185 sf0412121896 4 12131185 1.43E-11 NA
vg0416635232 sf0416463272 4 16635232 1.12E-10 1.00E-05
vg0508131496 sf0508131436 5 8131496 NA 3.08E-06