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 mr1383 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
vg0700233324 sf0700232324 7 233324 3.28E-11 2.22E-08
vg0700107355 sf0700106355 7 107355 1.25E-10 1.64E-08
vg1212172403 sf1212169740 12 12172403 9.44E-10 6.06E-07
vg0700250116 sf0700249116 7 250116 1.28E-09 5.22E-07
vg1207616892 sf1207614298 12 7616892 6.09E-09 7.10E-06
vg0700179866 sf0700178866 7 179866 8.11E-09 2.88E-06
vg1217438475 sf1217432430 12 17438475 2.21E-08 NA
vg1000080276 sf1000079276 10 80276 6.35E-08 1.74E-06
vg0900044105 sf0900043105 9 44105 7.69E-08 9.35E-07
vg0113613619 sf0113612593 1 13613619 2.04E-06 1.05E-07