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 mr1187 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
vg0712460832 sf0712459839 7 12460832 1.08E-07 1.08E-07
vg1110222856 sf1110217433 11 10222856 2.42E-07 2.42E-07
vg0626092324 sf0626091327 6 26092324 8.75E-07 8.75E-07
vg1119375564 sf1118909252 11 19375564 1.99E-06 1.99E-06
vg1223100837 sf1223067297 12 23100837 4.09E-06 4.09E-06
vg0324116929 sf0324115008 3 24116929 4.14E-06 4.14E-06
vg1117619488 sf1117153344 11 17619488 4.77E-06 4.78E-06
vg1119375243 sf1118908931 11 19375243 6.25E-06 6.25E-06