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 mr1153 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
vg0719513815 sf0719512822 7 19513815 2.20E-09 NA
vg1214625010 sf1214622350 12 14625010 2.37E-09 8.14E-06
vg1214656787 sf1214654127 12 14656787 7.86E-09 7.27E-06
vg1004396444 sf1004412982 10 4396444 2.02E-08 NA
vg0715474043 sf0715473050 7 15474043 2.44E-08 NA
vg1207510234 sf1207507640 12 7510234 3.03E-08 NA
vg0141145804 sf0141144761 1 41145804 1.52E-07 NA