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 mr1875 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
vg0123687464 sf0123686420 1 23687464 2.04E-11 NA
vg1126383521 sf1125911934 11 26383521 7.06E-11 NA
vg1127143286 sf1126671673 11 27143286 3.11E-10 NA
vg0516005213 sf0515947721 5 16005213 4.34E-10 9.13E-06
vg1126481520 sf1126009934 11 26481520 6.93E-10 NA
vg1126584071 sf1126112486 11 26584071 1.18E-08 1.79E-08
vg0122413949 sf0122412904 1 22413949 2.00E-06 6.20E-06