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 mr1021 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
vg0232621709 sf0232615840 2 32621709 1.46E-23 NA
vg0825909012 sf0825906298 8 25909012 2.30E-23 NA
vg0127650549 sf0127649505 1 27650549 3.87E-23 NA
vg1200188394 sf1200187394 12 188394 9.73E-23 NA
vg0620627981 sf0620626984 6 20627981 1.24E-22 NA
vg1004624542 sf1004641080 10 4624542 NA 1.60E-07
vg1222419954 sf1222386393 12 22419954 NA 1.63E-06
vg1217064292 sf1217058247 12 17064292 NA 2.93E-06
vg1222407299 sf1222373738 12 22407299 NA 3.69E-06
vg0609445027 sf0609444028 6 9445027 NA 4.14E-06