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 mr1976 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
vg0805900956 sf0805899959 8 5900956 4.08E-07 2.90E-07
vg0403709681 sf0403705287 4 3709681 1.84E-06 2.88E-06
vg0208626738 sf0208626737 2 8626738 4.06E-06 3.22E-06
vg1213717963 sf1213715301 12 13717963 8.24E-06 8.88E-07
vg0816083361 sf0816080647 8 16083361 NA 1.03E-06
vg0805970880 sf0805969883 8 5970880 NA 2.85E-06
vg0910442886 sf0910441885 9 10442886 NA 3.80E-06
vg0505749457 sf0505749395 5 5749457 NA 4.52E-06
vg0608868763 sf0608867764 6 8868763 NA 4.58E-06
vg1216757238 sf1216751192 12 16757238 NA 4.92E-06