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 mr1532 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
vg1118414920 sf1117948780 11 18414920 3.02E-09 NA
vg0314131280 sf0314129969 3 14131280 4.87E-09 NA
vg0818736737 sf0818734024 8 18736737 7.29E-09 NA
vg1000213979 sf1000212979 10 213979 8.11E-09 6.40E-06
vg0919770032 sf0919769551 9 19770032 8.74E-09 NA
vg1010348591 sf1010277412 10 10348591 1.49E-08 NA
vg1023134936 sf1023063408 10 23134936 1.26E-07 NA
vg0709128655 sf0709127661 7 9128655 2.51E-06 1.58E-06