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 mr1227 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
vg1214600105 sf1214597445 12 14600105 6.47E-11 1.71E-06
vg1223417517 sf1223383977 12 23417517 1.48E-10 NA
vg0222722732 sf0222716863 2 22722732 3.62E-10 NA
vg0222740991 sf0222735122 2 22740991 6.08E-10 NA
vg1217923635 sf1217895069 12 17923635 6.50E-10 NA
vg0226706895 sf0226701026 2 26706895 7.82E-10 NA
vg0622581962 sf0622580965 6 22581962 4.19E-08 NA
vg0234962638 sf0234956769 2 34962638 1.12E-07 NA
vg0719181533 sf0719180540 7 19181533 1.47E-07 4.25E-08
vg0213442655 sf0213442651 2 13442655 2.84E-07 NA
vg1214567309 sf1214564650 12 14567309 1.86E-06 NA
vg0315349460 sf0315348107 3 15349460 2.98E-06 5.85E-06
vg0719049906 sf0719048913 7 19049906 NA 7.32E-10
vg0719144835 sf0719143842 7 19144835 NA 4.58E-07
vg0113087370 sf0113086344 1 13087370 NA 2.25E-06
vg0820374974 sf0820372261 8 20374974 NA 3.56E-06
vg0314626927 sf0314625614 3 14626927 NA 4.25E-06
vg0315333930 sf0315332577 3 15333930 NA 4.68E-06