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 mr1870 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
vg0311708059 sf0311706777 3 11708059 7.14E-09 NA
vg0714411451 sf0714410458 7 14411451 9.20E-09 NA
vg0304178129 sf0304177131 3 4178129 1.10E-08 NA
vg0434808853 sf0434623744 4 34808853 1.15E-08 NA
vg0123380364 sf0123379320 1 23380364 1.88E-08 NA
vg0528627048 sf0528564403 5 28627048 3.34E-06 NA
vg0904895303 sf0904894303 9 4895303 5.19E-06 NA
vg0133431550 sf0133430506 1 33431550 5.87E-06 NA
vg1123918492 sf1123452362 11 23918492 NA 1.69E-06
vg1123877399 sf1123411269 11 23877399 NA 2.63E-06