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 mr1624 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
vg0710971660 sf0710970666 7 10971660 8.80E-12 NA
vg1000343179 sf1000342179 10 343179 4.32E-11 NA
vg0714562076 sf0714561083 7 14562076 4.31E-10 NA
vg0710495043 sf0710494049 7 10495043 1.06E-09 NA
vg1017975738 sf1017904510 10 17975738 2.37E-09 NA
vg0618168177 sf0618167180 6 18168177 3.09E-09 NA
vg1126042091 sf1125570505 11 26042091 NA 7.31E-06