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 mr1272 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
vg0330723756 sf0330716643 3 30723756 3.91E-21 7.47E-08
vg0330824541 sf0330817428 3 30824541 4.96E-21 1.74E-08
vg1105692960 sf1105688712 11 5692960 3.61E-17 NA
vg1217046946 sf1217040900 12 17046946 3.37E-15 NA
vg0507267164 sf0507267106 5 7267164 5.26E-15 NA
vg0428024263 sf0427839127 4 28024263 8.93E-15 NA
vg1103053214 sf1103049118 11 3053214 2.65E-14 4.82E-06
vg1103053231 sf1103049135 11 3053231 2.71E-14 4.20E-06