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 mr1583 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
vg0610144953 sf0610143954 6 10144953 1.26E-26 1.85E-14
vg0610549621 sf0610548622 6 10549621 1.97E-25 1.06E-14
vg0610492852 sf0610491853 6 10492852 5.96E-24 2.99E-14
vg0610590324 sf0610589325 6 10590324 1.70E-11 2.36E-06
vg0805557436 sf0805556439 8 5557436 4.72E-11 NA
vg0610769166 sf0610768167 6 10769166 1.07E-10 1.05E-06
vg0612914787 sf0612913788 6 12914787 1.72E-10 NA
vg0610457875 sf0610456876 6 10457875 1.08E-09 1.09E-08
vg0609807879 sf0609806880 6 9807879 1.84E-09 3.11E-06
vg0317228450 sf0317227260 3 17228450 1.08E-08 5.46E-07
vg0610680359 sf0610679360 6 10680359 1.03E-07 4.22E-07
vg0114537729 sf0114536703 1 14537729 6.59E-07 3.18E-06
vg0128147955 sf0128146911 1 28147955 8.60E-07 NA
vg0209742252 sf0209742250 2 9742252 NA 1.34E-06
vg0412908287 sf0412898995 4 12908287 NA 3.20E-06