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 mr1146 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
vg0222747179 sf0222741310 2 22747179 2.29E-24 6.48E-23
vg0222743526 sf0222737657 2 22743526 3.02E-24 5.21E-23
vg0222634177 sf0222628308 2 22634177 7.75E-11 4.46E-09
vg0223077654 sf0223071785 2 23077654 2.76E-09 8.11E-09
vg0223078170 sf0223072301 2 23078170 2.98E-09 9.21E-09
vg0222879623 sf0222873754 2 22879623 1.25E-08 3.00E-08
vg0222797604 sf0222791735 2 22797604 1.03E-07 4.83E-07
vg0224127834 sf0224121965 2 24127834 1.34E-07 1.61E-06
vg0222765370 sf0222759501 2 22765370 1.57E-07 3.94E-06
vg0224636312 sf0224630443 2 24636312 5.37E-07 8.11E-07
vg0223039697 sf0223033828 2 23039697 2.88E-06 8.98E-07
vg0222134940 sf0222129071 2 22134940 5.19E-06 3.58E-06