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 mr1824 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
vg0918774898 sf0918773898 9 18774898 1.17E-08 1.17E-08
vg0805108529 sf0805107532 8 5108529 6.38E-08 6.38E-08
vg0223170170 sf0223164301 2 23170170 3.37E-07 3.37E-07
vg0915815139 sf0915814138 9 15815139 3.87E-07 3.87E-07
vg0207694633 sf0207694632 2 7694633 4.96E-07 4.96E-07
vg1124247036 sf1123780906 11 24247036 5.26E-07 5.26E-07
vg1214703763 sf1214701104 12 14703763 9.09E-07 9.09E-07
vg0223074046 sf0223068177 2 23074046 1.85E-06 1.85E-06
vg0314986971 sf0314985618 3 14986971 2.67E-06 2.68E-06
vg0805900956 sf0805899959 8 5900956 3.25E-06 3.25E-06
vg0102103204 sf0102102204 1 2103204 4.67E-06 4.67E-06
vg1213717963 sf1213715301 12 13717963 6.49E-06 6.48E-06