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 mr1257 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
vg0216744504 sf0216738634 2 16744504 3.87E-11 8.12E-07
vg0718471109 sf0718470116 7 18471109 2.09E-08 NA
vg1127262549 sf1126790936 11 27262549 2.12E-08 NA
vg0718800424 sf0718799431 7 18800424 2.55E-08 NA
vg1215801176 sf1215798473 12 15801176 2.85E-08 NA
vg1218136630 sf1218108066 12 18136630 3.72E-08 1.53E-06
vg1211620649 sf1211617985 12 11620649 4.96E-06 1.04E-06