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 mr1230 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
vg1117172234 sf1116706086 11 17172234 1.75E-07 1.75E-07
vg1117087408 sf1116621260 11 17087408 2.52E-07 2.52E-07
vg0908892007 sf0908891006 9 8892007 1.00E-06 1.00E-06
vg1126855615 sf1126384002 11 26855615 1.33E-06 1.33E-06
vg0908891592 sf0908890591 9 8891592 2.70E-06 2.70E-06
vg0908683598 sf0908682597 9 8683598 3.16E-06 3.16E-06
vg0816082604 sf0816079890 8 16082604 3.62E-06 3.62E-06
vg0715227955 sf0715226962 7 15227955 3.66E-06 3.66E-06