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 mr1789 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
vg1200675049 sf1200674049 12 675049 8.68E-15 NA
vg0107825185 sf0107824185 1 7825185 3.72E-14 NA
vg1118315349 sf1117849207 11 18315349 3.97E-14 NA
vg0231891447 sf0231885578 2 31891447 5.18E-14 NA
vg0124625557 sf0124624513 1 24625557 5.66E-14 NA
vg0707996084 sf0707995089 7 7996084 7.46E-14 7.04E-06
vg0432917170 sf0432732057 4 32917170 4.37E-13 1.87E-07
vg0816279098 sf0816276384 8 16279098 3.60E-12 9.89E-07
vg0914463142 sf0914462141 9 14463142 2.39E-11 1.08E-06
vg0816276034 sf0816273320 8 16276034 NA 6.27E-08
vg1213709694 sf1213707032 12 13709694 NA 8.61E-08
vg0114563116 sf0114562090 1 14563116 NA 4.31E-06