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 mr1429 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
vg0200643756 sf0200643756 2 643756 3.76E-07 3.76E-07
vg0132416363 sf0132415319 1 32416363 2.29E-06 2.29E-06
vg1207276357 sf1207273764 12 7276357 3.11E-06 3.11E-06
vg1117569414 sf1117103271 11 17569414 3.61E-06 3.61E-06
vg0103007968 sf0103006968 1 3007968 3.89E-06 3.89E-06
vg0224868229 sf0224862360 2 24868229 4.26E-06 4.26E-06
vg0910768444 sf0910767443 9 10768444 4.50E-06 4.50E-06
vg0501529875 sf0501529859 5 1529875 4.58E-06 4.58E-06
vg1107376701 sf1107372446 11 7376701 4.62E-06 4.62E-06
vg1218273231 sf1218244667 12 18273231 8.18E-06 8.18E-06