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 mr1771 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
vg0821751104 sf0821748391 8 21751104 7.79E-10 NA
vg0123690615 sf0123689571 1 23690615 2.08E-09 NA
vg0131535738 sf0131534694 1 31535738 3.60E-09 NA
vg0218537804 sf0218531935 2 18537804 5.84E-09 NA
vg0725376215 sf0725375221 7 25376215 1.72E-08 NA
vg0131957102 sf0131956058 1 31957102 2.54E-08 9.39E-06
vg0330375659 sf0330368698 3 30375659 2.80E-08 NA
vg0718838390 sf0718837397 7 18838390 9.42E-07 3.25E-06
vg0103381628 sf0103380628 1 3381628 2.92E-06 NA