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 mr1805 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
vg0525533934 sf0525471355 5 25533934 3.35E-12 NA
vg0907968670 sf0907967670 9 7968670 3.54E-12 NA
vg0432784993 sf0432599879 4 32784993 1.52E-11 NA
vg1215794902 sf1215792199 12 15794902 1.98E-11 NA
vg1020611889 sf1020540368 10 20611889 2.11E-11 NA
vg1224473117 sf1224439571 12 24473117 2.57E-09 NA
vg0123086310 sf0123085266 1 23086310 2.60E-08 NA
vg0106285349 sf0106284349 1 6285349 5.20E-08 NA
vg0431151753 sf0430966644 4 31151753 NA 2.31E-06