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 mr1843 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
vg1215307750 sf1215305048 12 15307750 1.57E-08 5.72E-08
vg1020531763 sf1020460242 10 20531763 6.20E-08 4.84E-07
vg1020529341 sf1020457820 10 20529341 6.59E-08 4.83E-07
vg0817557507 sf0817554793 8 17557507 1.37E-07 4.09E-07
vg0420718113 sf0420546156 4 20718113 2.21E-07 2.84E-07
vg0223525077 sf0223519208 2 23525077 3.55E-07 2.62E-06
vg0516508609 sf0516451091 5 16508609 6.17E-07 1.03E-06
vg0235581681 sf0235575812 2 35581681 2.85E-06 2.84E-06
vg1104448944 sf1104444846 11 4448944 3.03E-06 1.87E-06
vg1209946884 sf1209944294 12 9946884 4.79E-06 4.55E-06
vg0113652030 sf0113651004 1 13652030 5.24E-06 4.15E-06
vg0608636014 sf0608635015 6 8636014 6.20E-06 3.92E-06
vg0620734924 sf0620733927 6 20734924 NA 3.01E-06
vg0902278490 sf0902277490 9 2278490 NA 3.56E-06
vg0424926413 sf0424741274 4 24926413 NA 4.72E-06