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 mr1136 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
vg0725004532 sf0725003538 7 25004532 6.74E-11 NA
vg0235365192 sf0235359323 2 35365192 8.64E-11 8.43E-06
vg0320074422 sf0320072933 3 20074422 1.32E-10 8.15E-06
vg0809642891 sf0809641895 8 9642891 1.44E-10 NA
vg0621856200 sf0621855203 6 21856200 2.75E-10 NA
vg1108064089 sf1108059834 11 8064089 6.29E-09 4.62E-06
vg0626829316 sf0626828319 6 26829316 1.56E-08 2.26E-06
vg0321811925 sf0321810435 3 21811925 2.04E-08 1.62E-06
vg0205760250 sf0205760250 2 5760250 NA 3.94E-07
vg0902265202 sf0902264202 9 2265202 NA 3.96E-07
vg1215354257 sf1215351555 12 15354257 NA 2.46E-06
vg0902265544 sf0902264544 9 2265544 NA 5.17E-06