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 mr1338 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
vg0414215680 sf0414206393 4 14215680 3.26E-10 NA
vg1002905822 sf1002904799 10 2905822 4.06E-10 NA
vg0910429389 sf0910428388 9 10429389 4.41E-10 NA
vg0907955125 sf0907954125 9 7955125 5.46E-10 NA
vg0122905275 sf0122904231 1 22905275 5.96E-10 NA
vg0910450391 sf0910449390 9 10450391 4.17E-09 NA
vg1122336896 sf1121870767 11 22336896 NA 2.86E-06
vg0101042259 sf0101041259 1 1042259 NA 4.49E-06