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 mr1180 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
vg0910844273 sf0910843272 9 10844273 6.08E-14 4.12E-06
vg0303827628 sf0303826624 3 3827628 5.94E-11 NA
vg0501173275 sf0501173259 5 1173275 2.16E-10 2.73E-06
vg0501172183 sf0501172167 5 1172183 6.45E-10 4.41E-06
vg0218451233 sf0218445364 2 18451233 1.31E-09 3.99E-07
vg0306755101 sf0306754101 3 6755101 2.28E-09 NA
vg0218455790 sf0218449921 2 18455790 1.67E-08 1.00E-07
vg0805022882 sf0805021885 8 5022882 9.17E-07 1.10E-06
vg0106203527 sf0106202527 1 6203527 1.33E-06 NA
vg0429371515 sf0429186381 4 29371515 8.84E-06 NA