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 mr1304 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
vg0723127888 sf0723126895 7 23127888 1.09E-08 3.01E-06
vg0723279532 sf0723278539 7 23279532 1.53E-08 1.64E-06
vg0209218990 sf0209218988 2 9218990 2.58E-07 1.82E-06
vg0619894737 sf0619893740 6 19894737 2.00E-06 2.86E-06
vg0114223167 sf0114222141 1 14223167 2.02E-06 4.17E-06
vg1214325834 sf1214323174 12 14325834 2.46E-06 4.80E-06
vg0911695608 sf0911694607 9 11695608 7.02E-06 1.39E-06