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 mr1826 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
vg0202440501 sf0202440499 2 2440501 5.76E-09 NA
vg1217857351 sf1217828785 12 17857351 8.72E-09 NA
vg0223727966 sf0223722097 2 23727966 1.03E-08 NA
vg0204065908 sf0204065905 2 4065908 1.71E-08 NA
vg1011365856 sf1011294675 10 11365856 3.02E-08 NA
vg1217856333 sf1217827767 12 17856333 3.30E-08 NA
vg1126117539 sf1125645953 11 26117539 9.08E-07 NA
vg0208715394 sf0208715393 2 8715394 2.89E-06 2.56E-06
vg1213930150 sf1213927488 12 13930150 4.78E-06 NA
vg1117649044 sf1117182900 11 17649044 NA 3.99E-06
vg1226241949 sf1226208343 12 26241949 NA 4.67E-06
vg1221594087 sf1221560634 12 21594087 NA 8.31E-06
vg0802945643 sf0802944646 8 2945643 NA 8.97E-06