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 mr1627 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
vg1217574896 sf1217568851 12 17574896 2.78E-12 2.68E-06
vg0726948774 sf0726947780 7 26948774 8.46E-12 NA
vg1217762938 sf1217706323 12 17762938 4.60E-11 1.20E-07
vg0724796245 sf0724795251 7 24796245 2.82E-10 NA
vg0908728928 sf0908727927 9 8728928 1.32E-09 NA
vg0616197348 sf0616196350 6 16197348 1.57E-09 NA
vg1117584893 sf1117118750 11 17584893 1.31E-07 6.66E-06
vg1210353594 sf1210351051 12 10353594 2.82E-07 NA
vg0910734911 sf0910733910 9 10734911 3.41E-06 3.97E-06
vg0722277880 sf0722276887 7 22277880 4.30E-06 NA