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 mr1377 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
vg0216998458 sf0216992588 2 16998458 4.41E-19 5.25E-10
vg0217022157 sf0217016287 2 17022157 9.19E-19 4.75E-10
vg0213525745 sf0213525741 2 13525745 1.01E-11 NA
vg0213138029 sf0213138025 2 13138029 4.44E-11 2.09E-06
vg0900336799 sf0900335799 9 336799 9.45E-10 NA
vg0216476829 sf0216470959 2 16476829 3.16E-09 NA
vg0335246131 sf0335239000 3 35246131 8.04E-09 NA
vg0216121800 sf0216115930 2 16121800 2.16E-08 4.55E-07
vg0719981901 sf0719980908 7 19981901 4.77E-07 NA
vg0608570503 sf0608569504 6 8570503 2.32E-06 NA