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 mr1574 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
vg0235128121 sf0235122252 2 35128121 2.46E-08 2.42E-06
vg0235123085 sf0235117216 2 35123085 3.15E-08 2.04E-06
vg0140618344 sf0140617301 1 40618344 7.35E-08 5.99E-07
vg0324328837 sf0324326916 3 24328837 1.12E-07 2.56E-06
vg0714415544 sf0714414551 7 14415544 3.01E-07 3.81E-06
vg1104316746 sf1104312648 11 4316746 1.03E-06 2.32E-06
vg1104316593 sf1104312495 11 4316593 3.24E-06 5.82E-06
vg1210552838 sf1210550251 12 10552838 5.35E-06 9.60E-06
vg0810864387 sf0810863392 8 10864387 5.76E-06 8.09E-06