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 mr1693 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
vg0519414866 sf0519352350 5 19414866 1.81E-13 NA
vg0432694084 sf0432508973 4 32694084 2.81E-13 9.53E-06
vg1204614801 sf1204613789 12 4614801 5.39E-13 3.94E-10
vg1017128609 sf1017057381 10 17128609 7.38E-13 2.02E-06
vg0502606736 sf0502606712 5 2606736 1.31E-12 8.92E-07
vg0516331935 sf0516274417 5 16331935 2.15E-12 3.12E-06
vg0519631422 sf0519568906 5 19631422 6.54E-12 8.85E-07
vg0910351895 sf0910350894 9 10351895 1.73E-11 1.11E-06
vg0302378820 sf0302377816 3 2378820 6.95E-11 2.37E-06
vg1117477253 sf1117011108 11 17477253 8.73E-11 NA
vg1016937957 sf1016866729 10 16937957 5.53E-10 1.80E-06
vg1121900686 sf1121434557 11 21900686 1.68E-09 1.65E-06
vg0920000635 sf0920000154 9 20000635 3.61E-09 NA
vg1204671475 sf1204670463 12 4671475 NA 1.42E-09
vg1204775308 sf1204774293 12 4775308 NA 9.13E-09
vg1218051198 sf1218022634 12 18051198 NA 1.38E-07
vg1204640879 sf1204639867 12 4640879 NA 1.61E-07
vg0404806537 sf0404801976 4 4806537 NA 2.10E-07
vg0134995977 sf0134994934 1 34995977 NA 4.51E-07
vg0916698836 sf0916697835 9 16698836 NA 6.74E-07
vg0625536742 sf0625535745 6 25536742 NA 7.01E-07
vg0129936226 sf0129935181 1 29936226 NA 1.06E-06
vg0423486114 sf0423300970 4 23486114 NA 1.44E-06
vg0107950946 sf0107949946 1 7950946 NA 1.81E-06
vg0434551164 sf0434366056 4 34551164 NA 2.31E-06
vg1204032367 sf1204031355 12 4032367 NA 3.15E-06
vg0134387944 sf0134386901 1 34387944 NA 3.93E-06
vg0906520037 sf0906519037 9 6520037 NA 4.31E-06