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 mr1392 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
vg1223970352 sf1223936805 12 23970352 3.37E-07 3.38E-07
vg0406413858 sf0406409298 4 6413858 4.76E-07 4.76E-07
vg0130154178 sf0130153133 1 30154178 5.21E-07 5.21E-07
vg0717069846 sf0717068853 7 17069846 9.42E-07 9.42E-07
vg0406094634 sf0406090073 4 6094634 9.81E-07 9.81E-07
vg0208547952 sf0208547951 2 8547952 1.50E-06 1.50E-06
vg1021192930 sf1021121408 10 21192930 1.86E-06 1.86E-06
vg1021465447 sf1021393924 10 21465447 2.45E-06 2.45E-06
vg1010619124 sf1010547945 10 10619124 3.88E-06 3.88E-06
vg0628274142 sf0628273144 6 28274142 4.52E-06 4.52E-06
vg1225469574 sf1225435969 12 25469574 4.67E-06 4.67E-06
vg0620614935 sf0620613938 6 20614935 4.70E-06 4.70E-06
vg0613877367 sf0613876368 6 13877367 4.97E-06 4.97E-06
vg0708274941 sf0708273946 7 8274941 4.98E-06 4.98E-06