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 mr1791 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
vg1122514350 sf1122048221 11 22514350 5.14E-09 6.32E-07
vg0224583319 sf0224577450 2 24583319 3.01E-08 8.47E-06
vg0800678290 sf0800677290 8 678290 3.81E-08 NA
vg0505704465 sf0505704403 5 5704465 7.02E-08 4.13E-06
vg0528402446 sf0528339801 5 28402446 1.16E-06 6.47E-06
vg0820759056 sf0820756343 8 20759056 7.57E-06 1.43E-06