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 mr1553 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
vg0621975537 sf0621974540 6 21975537 1.84E-10 1.29E-06
vg1211120342 sf1211117706 12 11120342 1.11E-09 5.42E-06
vg0522714833 sf0522652275 5 22714833 5.88E-09 NA
vg0218683444 sf0218677575 2 18683444 8.46E-09 NA
vg0901469520 sf0901468520 9 1469520 8.94E-09 NA
vg0402217448 sf0402213043 4 2217448 2.18E-08 3.29E-06