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 mr1169 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
vg0429941180 sf0429756047 4 29941180 5.05E-18 9.07E-10
vg0429928046 sf0429742913 4 29928046 6.32E-16 3.35E-10
vg0428010940 sf0427825804 4 28010940 4.37E-11 4.19E-06
vg0419105799 sf0418933837 4 19105799 6.09E-10 NA
vg0423314371 sf0423129226 4 23314371 1.58E-09 NA
vg0426455143 sf0426270015 4 26455143 4.47E-09 NA
vg0217962243 sf0217956374 2 17962243 1.10E-06 3.72E-06
vg0912289878 sf0912288877 9 12289878 3.03E-06 1.03E-06
vg0431612471 sf0431427366 4 31612471 5.60E-06 NA
vg1204378188 sf1204377176 12 4378188 NA 3.97E-06
vg0222503769 sf0222497900 2 22503769 NA 4.47E-06