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 mr1451 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
vg0414235746 sf0414226459 4 14235746 2.59E-09 5.83E-06
vg0315305972 sf0315304619 3 15305972 6.21E-08 NA
vg0518392219 sf0518331705 5 18392219 9.18E-08 NA
vg0728752228 sf0728751236 7 28752228 9.61E-08 NA
vg0414281024 sf0414271737 4 14281024 2.12E-07 NA
vg0104202598 sf0104201598 1 4202598 NA 5.97E-07
vg0205733501 sf0205733501 2 5733501 NA 2.97E-06