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 mr1268 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
vg1128243970 sf1127720749 11 28243970 1.36E-09 5.31E-06
vg1122861852 sf1122395723 11 22861852 6.20E-09 6.67E-06
vg1107186179 sf1107181924 11 7186179 1.07E-08 NA
vg1219228902 sf1219200372 12 19228902 1.39E-08 2.45E-06
vg1219213135 sf1219184605 12 19213135 2.29E-08 9.65E-07
vg1221819145 sf1221785692 12 21819145 4.51E-08 NA
vg0118434108 sf0118433062 1 18434108 1.77E-07 2.01E-06
vg1217635882 sf1217629837 12 17635882 2.49E-07 7.88E-07
vg0613089610 sf0613088611 6 13089610 3.62E-06 4.59E-06
vg0805516079 sf0805515082 8 5516079 4.39E-06 2.03E-06
vg0501563153 sf0501563137 5 1563153 NA 3.79E-06