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 mr1424 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
vg1114878427 sf1114414741 11 14878427 4.86E-07 4.86E-07
vg1216247174 sf1216244470 12 16247174 5.44E-07 5.45E-07
vg1215734129 sf1215731426 12 15734129 1.17E-06 1.17E-06
vg1013624010 sf1013552780 10 13624010 1.68E-06 1.68E-06
vg1208153687 sf1208151093 12 8153687 4.58E-06 4.58E-06
vg1006597026 sf1006612649 10 6597026 4.92E-06 4.92E-06