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 mr1154 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
vg0130670983 sf0130669939 1 30670983 1.30E-18 7.17E-15
vg0135821566 sf0135820523 1 35821566 3.98E-09 NA
vg1203606223 sf1203605222 12 3606223 4.05E-09 NA
vg1200417909 sf1200416909 12 417909 2.97E-08 NA
vg0130903912 sf0130902868 1 30903912 3.25E-08 NA
vg0401727352 sf0401722901 4 1727352 6.41E-08 3.31E-06
vg1226948201 sf1226914600 12 26948201 1.38E-07 5.74E-07
vg1226947846 sf1226914245 12 26947846 8.63E-07 3.31E-06
vg1101701811 sf1101700812 11 1701811 3.82E-06 NA
vg0130861999 sf0130860955 1 30861999 NA 1.05E-06
vg0129955088 sf0129954043 1 29955088 NA 1.75E-06
vg0708094466 sf0708093471 7 8094466 NA 4.55E-06