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 mr1863 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
vg1220236502 sf1220207944 12 20236502 6.32E-08 2.00E-07
vg1214365340 sf1214362680 12 14365340 6.98E-08 5.09E-07
vg0217031308 sf0217025438 2 17031308 3.70E-07 9.33E-07
vg1100523028 sf1100522031 11 523028 5.12E-07 4.53E-06
vg1105850724 sf1105846476 11 5850724 5.68E-07 NA
vg1117095528 sf1116629380 11 17095528 6.58E-07 4.48E-06