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 mr1194 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
vg0806712428 sf0806711433 8 6712428 2.65E-53 8.26E-06
vg0820710913 sf0820708200 8 20710913 1.21E-52 9.65E-06
vg0215052036 sf0215046166 2 15052036 3.35E-51 NA
vg0103472458 sf0103471458 1 3472458 6.42E-51 NA
vg0719848421 sf0719847428 7 19848421 7.54E-51 NA
vg0820733365 sf0820730652 8 20733365 6.14E-47 NA
vg0526975862 sf0526913218 5 26975862 NA 3.21E-10
vg0404463578 sf0404459182 4 4463578 NA 6.50E-08
vg0410059724 sf0410050421 4 10059724 NA 6.21E-07
vg0402400074 sf0402395669 4 2400074 NA 6.62E-07
vg0434732193 sf0434547084 4 34732193 NA 8.24E-07
vg0434702695 sf0434517584 4 34702695 NA 1.49E-06
vg0103416626 sf0103415626 1 3416626 NA 1.55E-06
vg0122460248 sf0122459203 1 22460248 NA 2.42E-06
vg1217915087 sf1217886521 12 17915087 NA 3.03E-06
vg0523999762 sf0523937182 5 23999762 NA 4.07E-06
vg0627902029 sf0627901031 6 27902029 NA 4.12E-06
vg0500963531 sf0500963514 5 963531 NA 7.37E-06