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 mr1881 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
vg0105287209 sf0105286209 1 5287209 8.31E-10 NA
vg0826973911 sf0826971197 8 26973911 9.52E-10 NA
vg0600058626 sf0600057626 6 58626 2.59E-09 NA
vg0112778994 sf0112777968 1 12778994 2.69E-09 NA
vg1218168020 sf1218139456 12 18168020 3.58E-09 NA
vg0501094691 sf0501094675 5 1094691 3.16E-08 NA
vg1218065136 sf1218036572 12 18065136 4.20E-08 4.96E-06
vg0322388599 sf0322387088 3 22388599 1.11E-07 NA
vg0827077651 sf0827074937 8 27077651 1.33E-06 NA
vg0615088126 sf0615087127 6 15088126 1.54E-06 NA
vg0713003786 sf0713002793 7 13003786 3.98E-06 NA
vg1214134669 sf1214132009 12 14134669 4.42E-06 3.30E-06
vg0621626147 sf0621625150 6 21626147 NA 2.61E-06
vg1214006412 sf1214003752 12 14006412 NA 8.53E-06