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 mr1833 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
vg1020531763 sf1020460242 10 20531763 2.18E-08 2.38E-07
vg0220342715 sf0220336847 2 20342715 3.20E-08 6.19E-06
vg0805992743 sf0805991746 8 5992743 5.82E-08 4.55E-06
vg0223525077 sf0223519208 2 23525077 9.70E-08 1.18E-06
vg1209946884 sf1209944294 12 9946884 3.16E-07 8.92E-07
vg0420718113 sf0420546156 4 20718113 4.11E-07 1.04E-06
vg0335297514 sf0335290383 3 35297514 4.32E-07 NA
vg0715010318 sf0715009325 7 15010318 1.22E-06 3.27E-06
vg1215307750 sf1215305048 12 15307750 1.47E-06 4.29E-06
vg0235581681 sf0235575812 2 35581681 1.60E-06 2.16E-06
vg0607826062 sf0607825063 6 7826062 8.51E-06 NA
vg0718397736 sf0718396743 7 18397736 NA 4.86E-07
vg0124441914 sf0124440870 1 24441914 NA 1.16E-06
vg0902278490 sf0902277490 9 2278490 NA 1.34E-06
vg0202017706 sf0202017706 2 2017706 NA 3.79E-06
vg0816931318 sf0816928604 8 16931318 NA 4.25E-06
vg0620734924 sf0620733927 6 20734924 NA 4.40E-06