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 mr1064 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
vg0916498845 sf0916497844 9 16498845 2.62E-12 4.99E-08
vg0430538314 sf0430353189 4 30538314 1.37E-11 2.88E-07
vg0114807948 sf0114806922 1 14807948 8.84E-10 NA
vg0434888110 sf0434703002 4 34888110 3.10E-09 NA
vg0225199712 sf0225193843 2 25199712 7.41E-09 NA
vg1127289309 sf1126817696 11 27289309 2.71E-07 4.84E-06
vg0412882680 sf0412873388 4 12882680 4.35E-06 NA
vg0218491418 sf0218485549 2 18491418 5.67E-06 3.55E-06
vg0620756988 sf0620755991 6 20756988 NA 7.52E-06