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 mr1156 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
vg0728156014 sf0728155021 7 28156014 1.75E-08 NA
vg0709448532 sf0709447538 7 9448532 2.84E-08 NA
vg0500057378 sf0500057378 5 57378 2.84E-08 8.30E-06
vg0502217293 sf0502217268 5 2217293 9.84E-08 NA
vg0727476091 sf0727475097 7 27476091 4.26E-07 NA
vg0307904502 sf0307903440 3 7904502 4.43E-07 4.24E-06
vg0229359655 sf0229353786 2 29359655 8.98E-07 2.66E-06
vg0727791830 sf0727790837 7 27791830 7.35E-06 NA
vg0516027523 sf0515970031 5 16027523 NA 2.80E-06
vg0515580789 sf0515523330 5 15580789 NA 4.14E-06