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 mr1413 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
vg0815689054 sf0815686340 8 15689054 1.30E-06 1.30E-06
vg1214199203 sf1214196543 12 14199203 1.44E-06 1.44E-06
vg1013742912 sf1013671681 10 13742912 2.72E-06 2.73E-06
vg0915815139 sf0915814138 9 15815139 3.13E-06 3.15E-06
vg0514228183 sf0514170726 5 14228183 4.70E-06 4.73E-06