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 mr1696 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
vg0729476993 sf0729476001 7 29476993 1.81E-10 NA
vg0218695086 sf0218689217 2 18695086 2.31E-10 NA
vg0126202736 sf0126201692 1 26202736 3.16E-10 NA
vg1216705859 sf1216699813 12 16705859 4.26E-10 NA
vg0232775464 sf0232769595 2 32775464 5.64E-10 NA
vg0100449701 sf0100448701 1 449701 3.63E-09 1.75E-07
vg0210599980 sf0210599978 2 10599980 3.83E-09 2.41E-06
vg1123051767 sf1122585638 11 23051767 4.98E-08 1.31E-06
vg0320631983 sf0320630493 3 20631983 3.31E-07 NA