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 mr1275 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
vg1219779242 sf1219750712 12 19779242 9.59E-10 7.94E-06
vg0139928356 sf0139927313 1 39928356 1.31E-09 NA
vg1215354383 sf1215351681 12 15354383 2.43E-09 NA
vg0518984986 sf0518922470 5 18984986 4.00E-09 NA
vg0914990285 sf0914989284 9 14990285 4.93E-09 NA
vg0230085254 sf0230079385 2 30085254 2.25E-08 NA
vg1215581638 sf1215578935 12 15581638 1.43E-06 NA
vg0432523363 sf0432338255 4 32523363 NA 2.42E-06
vg0115899007 sf0115897981 1 15899007 NA 2.46E-06
vg1214134657 sf1214131997 12 14134657 NA 4.65E-06