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 mr1637 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
vg1215125578 sf1215122914 12 15125578 5.29E-08 NA
vg0718838390 sf0718837397 7 18838390 7.79E-07 2.66E-06
vg0907175535 sf0907174535 9 7175535 1.21E-06 1.63E-06
vg0211842214 sf0211842210 2 11842214 1.38E-06 4.51E-07
vg0820948192 sf0820945479 8 20948192 1.93E-06 4.61E-06
vg0907175556 sf0907174556 9 7175556 3.74E-06 4.25E-06
vg0514453167 sf0514395710 5 14453167 NA 2.97E-06