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 mr1860 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
vg0918158744 sf0918157743 9 18158744 5.81E-28 1.32E-15
vg0916020326 sf0916019325 9 16020326 8.63E-17 NA
vg0333619008 sf0333611878 3 33619008 3.30E-16 3.24E-09
vg0604638830 sf0604637831 6 4638830 4.02E-13 NA
vg0611042230 sf0611041231 6 11042230 1.04E-12 NA
vg0222050955 sf0222045086 2 22050955 8.04E-12 1.17E-06
vg0332920303 sf0332913173 3 32920303 2.14E-11 3.92E-07
vg0323940115 sf0323938289 3 23940115 1.26E-09 NA
vg0617852939 sf0617851942 6 17852939 1.36E-08 4.54E-06
vg0333694886 sf0333687756 3 33694886 1.61E-08 8.15E-08
vg0916208687 sf0916207686 9 16208687 NA 8.66E-11
vg0916248949 sf0916247948 9 16248949 NA 8.59E-07
vg0332218798 sf0332211676 3 32218798 NA 8.86E-07
vg0428439422 sf0428254276 4 28439422 NA 1.08E-06
vg0332372666 sf0332365538 3 32372666 NA 1.11E-06
vg0812683923 sf0812681748 8 12683923 NA 1.15E-06
vg1013687229 sf1013615998 10 13687229 NA 1.70E-06
vg1207888410 sf1207885816 12 7888410 NA 1.96E-06
vg0608650270 sf0608649271 6 8650270 NA 2.09E-06
vg1102661323 sf1102657227 11 2661323 NA 2.89E-06
vg0219817547 sf0219811679 2 19817547 NA 3.58E-06
vg0613088823 sf0613087824 6 13088823 NA 3.60E-06
vg0617843171 sf0617842174 6 17843171 NA 3.67E-06
vg0607378850 sf0607377851 6 7378850 NA 3.69E-06
vg0820029453 sf0820026740 8 20029453 NA 4.47E-06
vg0412820231 sf0412810941 4 12820231 NA 4.47E-06
vg0333525256 sf0333518126 3 33525256 NA 4.74E-06
vg1210023864 sf1210021275 12 10023864 NA 5.83E-06