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 mr1915 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
vg0329146373 sf0329139425 3 29146373 3.26E-07 3.26E-07
vg0401799749 sf0401795344 4 1799749 5.39E-07 5.39E-07
vg1227287870 sf1227254270 12 27287870 6.26E-07 6.26E-07
vg0121172559 sf0121171514 1 21172559 8.65E-07 8.65E-07
vg0507826953 sf0507826894 5 7826953 1.30E-06 1.30E-06
vg0335027666 sf0335020536 3 35027666 1.57E-06 1.57E-06
vg1227357645 sf1227324045 12 27357645 1.66E-06 1.66E-06
vg0200274146 sf0200274146 2 274146 1.73E-06 1.73E-06
vg0620635407 sf0620634410 6 20635407 2.74E-06 2.74E-06
vg0826091106 sf0826088392 8 26091106 3.26E-06 3.26E-06
vg1116402406 sf1115937283 11 16402406 4.00E-06 4.00E-06