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 mr1653 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
vg1216247174 sf1216244470 12 16247174 7.80E-09 9.71E-06
vg1108548494 sf1108543104 11 8548494 1.99E-08 1.03E-06
vg0816292104 sf0816289390 8 16292104 4.27E-08 1.43E-06
vg1015796617 sf1015725387 10 15796617 8.13E-08 NA
vg0207830667 sf0207830666 2 7830667 1.00E-07 2.54E-06
vg1107500004 sf1107495749 11 7500004 NA 1.14E-06