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 mr1469 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
vg0822105767 sf0822103054 8 22105767 3.61E-10 2.91E-07
vg0821970212 sf0821967499 8 21970212 3.86E-10 2.43E-07
vg0139856883 sf0139855840 1 39856883 2.85E-08 NA
vg1214600105 sf1214597445 12 14600105 8.44E-08 1.48E-06
vg0126639023 sf0126637979 1 26639023 8.89E-08 NA
vg0211842214 sf0211842210 2 11842214 6.99E-07 1.10E-06
vg0130290451 sf0130289406 1 30290451 8.29E-06 NA
vg0822155831 sf0822153118 8 22155831 NA 1.77E-06
vg0127206110 sf0127205066 1 27206110 NA 4.45E-06