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 mr1181 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
vg0724529012 sf0724528018 7 24529012 1.82E-46 4.24E-16
vg0724528315 sf0724527321 7 24528315 2.42E-46 2.71E-16
vg0504620136 sf0504620113 5 4620136 1.42E-39 NA
vg1223869386 sf1223835839 12 23869386 9.30E-39 NA
vg0719369036 sf0719368043 7 19369036 1.09E-38 NA
vg0520313170 sf0520250643 5 20313170 1.37E-38 NA
vg0724504161 sf0724503167 7 24504161 NA 1.33E-11
vg0624461841 sf0624460844 6 24461841 NA 1.42E-07
vg0724376037 sf0724375043 7 24376037 NA 1.46E-07
vg0142357264 sf0142356220 1 42357264 NA 2.25E-07
vg0724425039 sf0724424045 7 24425039 NA 2.37E-07
vg0309318200 sf0309317136 3 9318200 NA 3.10E-07
vg1107663436 sf1107659181 11 7663436 NA 5.63E-07
vg0917635521 sf0917634520 9 17635521 NA 2.02E-06
vg0517583079 sf0517522722 5 17583079 NA 2.19E-06
vg0416107935 sf0415935968 4 16107935 NA 2.39E-06
vg1103318925 sf1103314828 11 3318925 NA 3.52E-06
vg0223219861 sf0223213992 2 23219861 NA 3.73E-06
vg0624474548 sf0624473551 6 24474548 NA 7.15E-06