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 mr1639 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
vg1214764189 sf1214761530 12 14764189 1.56E-08 7.71E-06
vg1211896931 sf1211894266 12 11896931 1.62E-08 2.93E-06
vg0529485802 sf0529423157 5 29485802 5.76E-07 NA
vg0218321013 sf0218315144 2 18321013 1.06E-06 NA
vg0210265227 sf0210265225 2 10265227 2.26E-06 4.87E-06
vg0109990052 sf0109989028 1 9990052 7.45E-06 NA
vg1109529032 sf1109523609 11 9529032 NA 6.55E-06