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 mr1479 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
vg0100929671 sf0100928671 1 929671 6.16E-10 NA
vg0329591518 sf0329584558 3 29591518 2.10E-09 NA
vg0123839187 sf0123838143 1 23839187 4.58E-09 NA
vg0139788105 sf0139787062 1 39788105 4.72E-09 NA
vg0200799086 sf0200799086 2 799086 5.25E-09 NA
vg0336243988 sf0336236914 3 36243988 7.33E-08 4.09E-07
vg1108050776 sf1108046521 11 8050776 9.04E-08 2.61E-06
vg0715376557 sf0715375564 7 15376557 1.10E-07 NA
vg0142259792 sf0142258748 1 42259792 1.13E-06 NA
vg0200335580 sf0200335580 2 335580 2.94E-06 NA
vg1007480591 sf1007496214 10 7480591 3.55E-06 3.80E-06
vg0413426469 sf0413417183 4 13426469 7.65E-06 NA
vg0916243238 sf0916242237 9 16243238 NA 2.85E-06
vg0614629248 sf0614628249 6 14629248 NA 4.67E-06