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 mr1254 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
vg0420739904 sf0420567947 4 20739904 1.07E-06 1.07E-06
vg0420295257 sf0420123302 4 20295257 1.40E-06 1.40E-06
vg0420556306 sf0420384350 4 20556306 1.54E-06 1.54E-06
vg0413297327 sf0413288038 4 13297327 2.19E-06 2.19E-06
vg0622417280 sf0622416283 6 22417280 2.25E-06 2.25E-06
vg0705311222 sf0705310223 7 5311222 2.88E-06 2.88E-06
vg0103511143 sf0103510143 1 3511143 3.58E-06 3.58E-06
vg0430344329 sf0430159206 4 30344329 3.98E-06 3.98E-06
vg0207077547 sf0207077547 2 7077547 4.13E-06 4.13E-06
vg0304381136 sf0304380138 3 4381136 4.30E-06 4.30E-06
vg0130552443 sf0130551399 1 30552443 4.48E-06 4.49E-06