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 mr1772 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
vg0604300121 sf0604299122 6 4300121 1.56E-08 8.06E-06
vg1117491108 sf1117024963 11 17491108 5.89E-08 NA
vg1200180642 sf1200179642 12 180642 9.47E-08 NA
vg1223454479 sf1223420939 12 23454479 6.28E-06 NA
vg1226056282 sf1226022676 12 26056282 NA 5.75E-07
vg1121116792 sf1120650671 11 21116792 NA 2.54E-06
vg0108656918 sf0108655918 1 8656918 NA 4.02E-06
vg1217812137 sf1217783571 12 17812137 NA 4.08E-06
vg1002941211 sf1002940188 10 2941211 NA 8.89E-06