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 mr1800 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
vg0432426919 sf0432241810 4 32426919 4.56E-16 1.69E-11
vg1018636735 sf1018565292 10 18636735 1.03E-08 5.82E-08
vg0800517477 sf0800516477 8 517477 1.12E-08 NA
vg0800502770 sf0800501770 8 502770 1.49E-08 NA
vg0516079925 sf0516022409 5 16079925 1.90E-08 NA
vg0516367809 sf0516310291 5 16367809 1.66E-07 5.01E-07
vg1122240342 sf1121774213 11 22240342 2.36E-07 2.91E-06
vg1018567276 sf1018495833 10 18567276 4.60E-07 2.74E-08
vg1117979612 sf1117513470 11 17979612 5.44E-07 7.03E-08
vg1018570407 sf1018498964 10 18570407 8.88E-07 7.62E-08
vg0800529132 sf0800528132 8 529132 1.39E-06 4.85E-06
vg1117980116 sf1117513974 11 17980116 3.88E-06 5.03E-08
vg0432443771 sf0432258662 4 32443771 NA 7.27E-07
vg1118091589 sf1117625447 11 18091589 NA 9.54E-07