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 mr1482 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
vg0809652916 sf0809651920 8 9652916 7.42E-08 NA
vg0816276034 sf0816273320 8 16276034 9.10E-07 2.53E-06
vg0422730303 sf0422545186 4 22730303 1.44E-06 NA
vg0414249582 sf0414240295 4 14249582 1.58E-06 2.65E-06
vg0608241022 sf0608240023 6 8241022 6.57E-06 9.21E-06
vg1006743978 sf1006759601 10 6743978 NA 8.27E-07