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 mr1786 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
vg0430980193 sf0430795073 4 30980193 1.30E-10 1.85E-06
vg0902627466 sf0902626466 9 2627466 3.02E-10 2.94E-06
vg0133432014 sf0133430970 1 33432014 4.53E-10 NA
vg0414484644 sf0414475358 4 14484644 4.77E-10 NA
vg0316612389 sf0316611034 3 16612389 5.70E-10 NA
vg0620613402 sf0620612405 6 20613402 1.12E-09 3.28E-06
vg0622667500 sf0622666503 6 22667500 3.70E-08 9.50E-06
vg0432523372 sf0432338264 4 32523372 2.69E-07 3.55E-07
vg0825053682 sf0825050968 8 25053682 9.80E-07 3.32E-06
vg0819529346 sf0819526633 8 19529346 NA 3.54E-06
vg0403566373 sf0403561975 4 3566373 NA 4.19E-06