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 mr1359 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
vg0122456656 sf0122455611 1 22456656 1.14E-09 NA
vg0414281024 sf0414271737 4 14281024 2.07E-09 4.85E-06
vg1016425716 sf1016354490 10 16425716 4.11E-09 NA
vg0314984669 sf0314983316 3 14984669 4.77E-08 NA
vg0103221429 sf0103220429 1 3221429 1.28E-06 8.15E-07
vg0414202857 sf0414193573 4 14202857 4.01E-06 3.84E-06
vg1114877180 sf1114413494 11 14877180 NA 2.15E-06