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 mr1248 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
vg0216763637 sf0216757767 2 16763637 3.84E-11 1.72E-06
vg1219345800 sf1219317270 12 19345800 4.14E-11 NA
vg0216713293 sf0216707423 2 16713293 1.06E-10 1.32E-06
vg0901298066 sf0901297066 9 1298066 2.38E-10 3.48E-07
vg0506159272 sf0506159211 5 6159272 9.56E-10 NA
vg0434375534 sf0434190428 4 34375534 1.40E-09 NA
vg0410044585 sf0410035282 4 10044585 2.58E-09 2.41E-07
vg1216567539 sf1216564832 12 16567539 9.21E-09 4.57E-06
vg1218508170 sf1218479606 12 18508170 1.59E-07 3.76E-06