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 mr1575 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
vg0711354697 sf0711353703 7 11354697 4.08E-08 4.08E-08
vg0230036530 sf0230030661 2 30036530 2.26E-07 2.26E-07
vg0715211021 sf0715210028 7 15211021 3.49E-07 3.50E-07
vg0714854525 sf0714853532 7 14854525 1.02E-06 1.02E-06
vg0205646080 sf0205646080 2 5646080 1.17E-06 1.17E-06
vg0716086571 sf0716085578 7 16086571 1.59E-06 1.59E-06
vg0816140925 sf0816138211 8 16140925 2.66E-06 2.66E-06
vg0528402446 sf0528339801 5 28402446 3.89E-06 3.89E-06
vg0706683462 sf0706682467 7 6683462 4.40E-06 4.40E-06