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 mr1813 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
vg1217711180 sf1217705135 12 17711180 5.42E-09 NA
vg0721356842 sf0721355849 7 21356842 5.67E-08 NA
vg1124617651 sf1124151491 11 24617651 9.75E-08 9.84E-06
vg0207690117 sf0207690117 2 7690117 7.08E-07 2.58E-06
vg0432523363 sf0432338255 4 32523363 7.26E-07 1.23E-06
vg0432523372 sf0432338264 4 32523372 1.15E-06 2.13E-06
vg0916030541 sf0916029540 9 16030541 3.91E-06 3.71E-06
vg0400149978 sf0400148978 4 149978 NA 2.04E-07