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 mr1424 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
vg1114911197 sf1114447511 11 14911197 8.92E-10 3.43E-07
vg1013390665 sf1013319435 10 13390665 1.82E-09 5.04E-06
vg1122514350 sf1122048221 11 22514350 1.01E-08 NA
vg1022178256 sf1022106730 10 22178256 1.14E-08 NA
vg0112354516 sf0112353490 1 12354516 1.35E-08 NA
vg1013475370 sf1013404140 10 13475370 2.16E-08 5.83E-06
vg0313065112 sf0313063830 3 13065112 3.26E-08 NA
vg1219410821 sf1219382291 12 19410821 1.45E-07 2.16E-06