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 mr1577 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
vg1215970970 sf1215968266 12 15970970 7.13E-13 1.79E-08
vg1210519897 sf1210517310 12 10519897 8.92E-11 2.97E-07
vg1210023864 sf1210021275 12 10023864 1.08E-10 1.26E-08
vg0216525301 sf0216519431 2 16525301 2.30E-10 9.82E-08
vg1215609371 sf1215606668 12 15609371 3.07E-08 NA
vg1215706891 sf1215704188 12 15706891 1.25E-07 3.21E-06
vg0503485496 sf0503485473 5 3485496 4.95E-07 3.52E-06
vg1106210872 sf1106206624 11 6210872 1.29E-06 2.86E-07
vg0218787476 sf0218781607 2 18787476 1.61E-06 NA
vg1215007375 sf1215004717 12 15007375 9.29E-06 3.87E-06
vg0607507935 sf0607506936 6 7507935 NA 4.96E-06