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 mr1072 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
vg0433014019 sf0432828905 4 33014019 7.82E-10 3.90E-06
vg0623955389 sf0623954392 6 23955389 9.06E-10 NA
vg0920872974 sf0920872493 9 20872974 7.72E-09 NA
vg0306892285 sf0306891283 3 6892285 7.82E-09 NA
vg0316346281 sf0316344928 3 16346281 1.23E-08 6.53E-06
vg0316345474 sf0316344121 3 16345474 1.31E-08 4.11E-06
vg1109134145 sf1109128724 11 9134145 1.41E-08 5.37E-07
vg0432765450 sf0432580336 4 32765450 6.07E-08 6.28E-07
vg0421350588 sf0421178642 4 21350588 2.71E-07 3.44E-06
vg0404447879 sf0404443483 4 4447879 6.99E-07 NA