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 mr1711 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
vg0431894969 sf0431709864 4 31894969 1.59E-10 3.08E-06
vg1215178307 sf1215175643 12 15178307 5.74E-10 9.05E-06
vg0113561451 sf0113560425 1 13561451 5.47E-09 NA
vg0722678256 sf0722677263 7 22678256 1.79E-08 NA
vg0118123199 sf0118122153 1 18123199 2.09E-08 NA
vg1204260659 sf1204259647 12 4260659 2.47E-08 6.06E-07
vg0116417409 sf0116416383 1 16417409 9.39E-08 NA
vg1224439207 sf1224405660 12 24439207 5.91E-07 2.28E-06
vg0718147951 sf0718146958 7 18147951 1.56E-06 NA
vg0910064812 sf0910063811 9 10064812 4.10E-06 9.18E-07