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 mr1093 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
vg0216746978 sf0216741108 2 16746978 3.92E-92 2.94E-25
vg0402172640 sf0402168235 4 2172640 6.38E-59 1.75E-07
vg0719539069 sf0719538076 7 19539069 3.45E-56 NA
vg0128294215 sf0128293171 1 28294215 3.92E-56 NA
vg0519475767 sf0519413251 5 19475767 8.73E-56 NA
vg0216804396 sf0216798526 2 16804396 NA 4.83E-17
vg0216636079 sf0216630209 2 16636079 NA 2.75E-08
vg0213525745 sf0213525741 2 13525745 NA 1.51E-06
vg0431613586 sf0431428481 4 31613586 NA 1.66E-06
vg0410044585 sf0410035282 4 10044585 NA 3.07E-06
vg0826171301 sf0826168587 8 26171301 NA 3.46E-06
vg0525571168 sf0525508589 5 25571168 NA 3.64E-06
vg0217266536 sf0217260666 2 17266536 NA 3.82E-06
vg0502171217 sf0502171192 5 2171217 NA 4.99E-06