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 mr1041 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 4.98E-07 4.98E-07
vg0220429795 sf0220423927 2 20429795 5.68E-07 5.68E-07
vg0314986971 sf0314985618 3 14986971 8.30E-07 8.30E-07
vg0805108529 sf0805107532 8 5108529 2.29E-06 2.29E-06
vg0220319668 sf0220313800 2 20319668 3.88E-06 3.88E-06
vg1213065934 sf1213063273 12 13065934 4.05E-06 4.05E-06
vg0232486002 sf0232480133 2 32486002 5.12E-06 5.12E-06