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 mr1795 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
vg0222738038 sf0222732169 2 22738038 1.13E-17 7.58E-13
vg0224622358 sf0224616489 2 24622358 1.12E-14 1.81E-10
vg0224620773 sf0224614904 2 24620773 6.40E-14 3.48E-11
vg0223635846 sf0223629977 2 23635846 4.79E-10 1.33E-06
vg0223943227 sf0223937358 2 23943227 7.31E-10 NA
vg0223169280 sf0223163411 2 23169280 2.82E-09 4.99E-06
vg0223637309 sf0223631440 2 23637309 5.06E-09 NA
vg1112909023 sf1112445344 11 12909023 1.99E-08 1.41E-08
vg0809640950 sf0809639954 8 9640950 7.22E-08 3.06E-06
vg0105681296 sf0105680296 1 5681296 2.85E-07 4.64E-07
vg0217679973 sf0217674103 2 17679973 3.42E-07 2.69E-06
vg0106725386 sf0106724386 1 6725386 9.07E-07 1.44E-06
vg0224574434 sf0224568565 2 24574434 1.49E-06 9.62E-07
vg0223007008 sf0223001139 2 23007008 5.09E-06 3.93E-06
vg0140082114 sf0140081071 1 40082114 9.19E-06 NA