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 mr1845 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
vg0225541312 sf0225535443 2 25541312 8.14E-10 1.05E-06
vg0319794993 sf0319793504 3 19794993 1.81E-09 NA
vg0320989254 sf0320987764 3 20989254 1.95E-09 3.27E-07
vg0215285143 sf0215279273 2 15285143 2.60E-09 NA
vg0802601304 sf0802600307 8 2601304 3.27E-09 NA
vg1224334241 sf1224300694 12 24334241 8.67E-09 NA
vg1216843085 sf1216837039 12 16843085 2.25E-08 4.72E-06
vg1125214331 sf1124748171 11 25214331 7.49E-08 NA
vg1206202617 sf1206201507 12 6202617 NA 8.03E-07
vg0420952139 sf0420780194 4 20952139 NA 8.84E-07