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 mr1560 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
vg0719001862 sf0719000869 7 19001862 7.06E-21 2.00E-15
vg0719250979 sf0719249986 7 19250979 2.95E-14 5.17E-08
vg1201736678 sf1201735676 12 1736678 3.35E-13 2.39E-07
vg0717368185 sf0717367192 7 17368185 1.21E-12 7.87E-07
vg0717227488 sf0717226495 7 17227488 1.08E-11 2.88E-06
vg0717375246 sf0717374253 7 17375246 2.25E-11 5.04E-07
vg1215637989 sf1215635286 12 15637989 3.40E-09 NA
vg0719465974 sf0719464981 7 19465974 4.70E-09 1.33E-07
vg0612586290 sf0612585291 6 12586290 6.30E-09 1.09E-06
vg0613063818 sf0613062819 6 13063818 2.68E-08 2.62E-06
vg0612290452 sf0612289453 6 12290452 2.90E-08 1.95E-06
vg0228211458 sf0228205589 2 28211458 4.08E-08 2.71E-06
vg0704472424 sf0704471425 7 4472424 1.98E-07 NA
vg1218127441 sf1218098877 12 18127441 6.50E-07 NA
vg0504291251 sf0504291228 5 4291251 1.42E-06 3.46E-06
vg0809647546 sf0809646550 8 9647546 1.94E-06 NA
vg0718964255 sf0718963262 7 18964255 NA 5.71E-07
vg0407629243 sf0407624510 4 7629243 NA 3.12E-06