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 mr1352 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
vg0138561974 sf0138560931 1 38561974 4.46E-17 NA
vg0306294140 sf0306293140 3 6294140 1.86E-16 NA
vg0132722397 sf0132721353 1 32722397 1.48E-15 NA
vg0123705252 sf0123704208 1 23705252 1.98E-15 NA
vg0130131012 sf0130129967 1 30131012 4.40E-15 NA
vg0526824051 sf0526761409 5 26824051 4.47E-13 4.49E-06
vg1214526344 sf1214523685 12 14526344 3.72E-11 1.58E-06
vg0318823675 sf0318822435 3 18823675 NA 1.95E-06
vg0210641169 sf0210641167 2 10641169 NA 3.79E-06