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 mr1942 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
vg1216469080 sf1216466373 12 16469080 2.13E-09 NA
vg0727131485 sf0727130491 7 27131485 3.20E-09 6.43E-06
vg1128770725 sf1128247504 11 28770725 6.16E-09 NA
vg1207920441 sf1207917847 12 7920441 9.12E-09 NA
vg0801223131 sf0801222133 8 1223131 1.00E-08 NA
vg0801815194 sf0801814197 8 1815194 2.08E-08 NA
vg0434375566 sf0434190460 4 34375566 1.13E-07 NA
vg1002656443 sf1002655420 10 2656443 NA 2.55E-06