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 mr1911 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
vg0222739831 sf0222733962 2 22739831 2.33E-33 5.50E-36
vg0222725003 sf0222719134 2 22725003 3.05E-21 2.32E-13
vg1009173095 sf1009101916 10 9173095 2.50E-20 NA
vg0906971590 sf0906970590 9 6971590 4.56E-20 NA
vg1201239657 sf1201238657 12 1239657 7.31E-20 NA
vg0222679274 sf0222673405 2 22679274 1.41E-19 7.53E-07
vg1202206315 sf1202205314 12 2206315 1.34E-16 NA
vg0224540602 sf0224534733 2 24540602 NA 6.88E-09
vg0221562295 sf0221556426 2 21562295 NA 2.46E-07
vg0222630293 sf0222624424 2 22630293 NA 4.62E-07
vg0222681985 sf0222676116 2 22681985 NA 5.63E-07
vg0224793596 sf0224787727 2 24793596 NA 1.35E-06
vg0233671295 sf0233665426 2 33671295 NA 1.68E-06
vg0202763283 sf0202763281 2 2763283 NA 2.04E-06
vg0119929841 sf0119928796 1 19929841 NA 3.89E-06
vg0816709248 sf0816706534 8 16709248 NA 4.35E-06