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 mr1075 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
vg0623955389 sf0623954392 6 23955389 3.67E-09 NA
vg0528836055 sf0528773410 5 28836055 5.28E-09 NA
vg0316345474 sf0316344121 3 16345474 7.19E-09 1.09E-06
vg0809725087 sf0809724091 8 9725087 3.42E-08 NA
vg0432961214 sf0432776101 4 32961214 3.99E-08 NA
vg1109134145 sf1109128724 11 9134145 4.87E-08 1.25E-06
vg0228232599 sf0228226730 2 28232599 8.75E-08 1.24E-06
vg0129740811 sf0129739766 1 29740811 1.12E-07 4.02E-06
vg0432877331 sf0432692218 4 32877331 1.60E-06 NA
vg0432698675 sf0432513565 4 32698675 2.68E-06 NA