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 mr1570 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
vg0609097640 sf0609096641 6 9097640 1.91E-13 4.05E-10
vg0319643905 sf0319642416 3 19643905 1.45E-10 2.03E-07
vg0208132368 sf0208132367 2 8132368 1.63E-09 6.31E-08
vg0916689643 sf0916688642 9 16689643 6.77E-09 7.61E-06
vg0208125954 sf0208125953 2 8125954 8.06E-09 1.63E-08
vg0922309029 sf0922308548 9 22309029 9.73E-09 3.32E-06
vg0608390668 sf0608389669 6 8390668 1.30E-08 3.03E-06
vg0609250230 sf0609249231 6 9250230 4.45E-08 1.75E-06
vg0207732987 sf0207732986 2 7732987 1.11E-07 4.89E-08
vg0404963883 sf0404959322 4 4963883 1.68E-07 2.32E-07
vg0208872595 sf0208872593 2 8872595 1.00E-06 7.85E-07
vg0100639439 sf0100638439 1 639439 1.81E-06 NA
vg0900102817 sf0900101817 9 102817 NA 2.59E-06
vg1000960938 sf1000959914 10 960938 NA 3.90E-06
vg0610749134 sf0610748135 6 10749134 NA 4.63E-06