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 mr1056 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
vg1208206256 sf1208203661 12 8206256 2.15E-18 3.09E-06
vg1016262709 sf1016191484 10 16262709 5.12E-18 6.29E-07
vg0129164753 sf0129163708 1 29164753 9.54E-18 NA
vg1215005384 sf1215002726 12 15005384 1.74E-17 7.79E-07
vg1216893534 sf1216887488 12 16893534 6.07E-17 9.56E-07
vg0434000706 sf0433815599 4 34000706 2.95E-16 5.42E-10
vg0526901536 sf0526838893 5 26901536 2.58E-15 2.38E-07
vg1216893818 sf1216887772 12 16893818 7.82E-15 2.11E-06
vg1209270443 sf1209267853 12 9270443 3.15E-14 1.92E-07
vg1208263364 sf1208260769 12 8263364 5.39E-13 1.93E-06
vg1015803765 sf1015732535 10 15803765 NA 5.93E-07
vg1020760386 sf1020688865 10 20760386 NA 7.09E-07
vg1020839196 sf1020767675 10 20839196 NA 8.44E-07
vg0905473217 sf0905472217 9 5473217 NA 1.10E-06
vg0713442761 sf0713441768 7 13442761 NA 2.35E-06
vg1121210363 sf1120744241 11 21210363 NA 3.16E-06