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 mr1663 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
vg0718568267 sf0718567274 7 18568267 2.96E-09 2.96E-09
vg0129591345 sf0129590300 1 29591345 5.64E-08 5.64E-08
vg1210393974 sf1210391387 12 10393974 1.44E-07 1.44E-07
vg0722028662 sf0722027669 7 22028662 2.17E-07 2.17E-07
vg0414596511 sf0414587225 4 14596511 2.33E-07 2.33E-07
vg0432785736 sf0432600622 4 32785736 4.50E-07 4.50E-07
vg1215527241 sf1215524538 12 15527241 5.08E-07 5.08E-07
vg0616076791 sf0616075793 6 16076791 8.58E-07 8.58E-07
vg0406002110 sf0405997550 4 6002110 9.00E-07 9.00E-07
vg0602175867 sf0602174868 6 2175867 1.08E-06 1.08E-06
vg0620620871 sf0620619874 6 20620871 1.11E-06 1.11E-06
vg1200586913 sf1200585913 12 586913 1.63E-06 1.63E-06
vg0230814769 sf0230808900 2 30814769 1.92E-06 1.92E-06
vg1000277307 sf1000276307 10 277307 2.33E-06 2.33E-06
vg0111138678 sf0111137654 1 11138678 2.54E-06 2.55E-06
vg0712895377 sf0712894384 7 12895377 2.69E-06 2.69E-06
vg0401649161 sf0401644710 4 1649161 2.96E-06 2.96E-06
vg1020767761 sf1020696240 10 20767761 3.08E-06 3.09E-06
vg1111006518 sf1111000835 11 11006518 3.08E-06 3.09E-06
vg0719056367 sf0719055374 7 19056367 4.01E-06 4.01E-06