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 mr1808 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
vg1009896954 sf1009825775 10 9896954 3.30E-09 NA
vg0902040540 sf0902039540 9 2040540 4.17E-09 9.70E-06
vg0527049134 sf0526986490 5 27049134 6.86E-09 NA
vg0122336970 sf0122335925 1 22336970 8.35E-09 1.82E-06
vg0233733433 sf0233727564 2 33733433 8.60E-09 NA
vg1125166964 sf1124700804 11 25166964 1.87E-06 8.90E-07
vg0908831499 sf0908830498 9 8831499 8.77E-06 NA
vg0709921514 sf0709920520 7 9921514 9.24E-06 NA
vg1200183647 sf1200182647 12 183647 NA 2.24E-07
vg0922613922 sf0922613441 9 22613922 NA 3.15E-06