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 mr1479 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
vg0619155361 sf0619154364 6 19155361 2.00E-08 8.33E-06
vg0619405763 sf0619404766 6 19405763 6.34E-08 7.58E-07
vg0920389319 sf0920388838 9 20389319 7.30E-08 NA
vg0419763927 sf0419591962 4 19763927 7.15E-07 3.50E-07
vg0618589804 sf0618588807 6 18589804 4.02E-06 NA