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 mr1852 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
vg0810647541 sf0810646545 8 10647541 8.29E-07 8.29E-07
vg1213459961 sf1213457299 12 13459961 8.86E-07 8.86E-07
vg1208226380 sf1208223785 12 8226380 1.19E-06 1.19E-06
vg1006743978 sf1006759601 10 6743978 1.44E-06 1.44E-06
vg0816101264 sf0816098550 8 16101264 1.76E-06 1.76E-06
vg1000804159 sf1000803135 10 804159 3.69E-06 3.69E-06
vg0805959254 sf0805958257 8 5959254 6.67E-06 6.67E-06