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 mr1438 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
vg0703027716 sf0703026717 7 3027716 1.69E-08 NA
vg1117249110 sf1116782962 11 17249110 2.14E-08 NA
vg0818648206 sf0818645493 8 18648206 2.32E-08 NA
vg0623104065 sf0623103068 6 23104065 2.58E-08 NA
vg0504837001 sf0504836978 5 4837001 3.02E-08 NA
vg0225800282 sf0225794413 2 25800282 4.16E-08 NA
vg0124667372 sf0124666328 1 24667372 3.53E-07 2.50E-07
vg0124656601 sf0124655557 1 24656601 4.03E-07 3.94E-07
vg0429686232 sf0429501100 4 29686232 7.32E-07 4.96E-07
vg0400770969 sf0400769969 4 770969 6.56E-06 2.53E-06
vg1215800897 sf1215798194 12 15800897 NA 1.26E-06
vg0720001612 sf0720000619 7 20001612 NA 2.71E-06
vg0230288823 sf0230282954 2 30288823 NA 2.77E-06