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 mr1297 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
vg1223091848 sf1223058308 12 23091848 2.38E-08 2.66E-06
vg1117625330 sf1117159186 11 17625330 4.94E-08 NA
vg0405832157 sf0405827596 4 5832157 7.84E-08 NA
vg0826159859 sf0826157145 8 26159859 1.73E-06 NA
vg0135430076 sf0135429033 1 35430076 3.75E-06 NA
vg1218162368 sf1218133804 12 18162368 NA 4.10E-06
vg0402100710 sf0402096304 4 2100710 NA 4.32E-06