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 mr1610 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
vg0217093910 sf0217088040 2 17093910 1.15E-19 3.47E-12
vg0217321139 sf0217315269 2 17321139 4.52E-14 6.78E-09
vg0217093377 sf0217087507 2 17093377 4.59E-14 3.72E-12
vg0217084511 sf0217078641 2 17084511 4.93E-14 1.08E-12
vg1215665438 sf1215662735 12 15665438 1.73E-11 NA
vg0908600483 sf0908599482 9 8600483 1.18E-10 NA
vg1013482552 sf1013411322 10 13482552 2.37E-10 NA
vg0423923614 sf0423738474 4 23923614 3.54E-10 4.81E-06
vg1220336402 sf1220307844 12 20336402 1.46E-09 3.16E-07
vg0217843760 sf0217837891 2 17843760 3.02E-08 3.64E-06
vg0216573861 sf0216567991 2 16573861 NA 1.23E-07
vg1128516527 sf1127993306 11 28516527 NA 1.44E-06
vg0902154424 sf0902153424 9 2154424 NA 2.12E-06
vg0216594873 sf0216589003 2 16594873 NA 4.44E-06