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 mr1161 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
vg1009703721 sf1009632542 10 9703721 1.54E-27 1.10E-09
vg1006731965 sf1006747588 10 6731965 2.93E-26 2.84E-12
vg1009147351 sf1009076212 10 9147351 4.93E-25 1.47E-12
vg0407823811 sf0407819079 4 7823811 1.38E-24 7.31E-07
vg1006556408 sf1006572031 10 6556408 1.89E-24 1.09E-15
vg0407825943 sf0407821211 4 7825943 8.88E-24 2.63E-07
vg1202107188 sf1202106186 12 2107188 5.11E-23 1.12E-06
vg0528707182 sf0528644537 5 28707182 7.19E-22 5.18E-07
vg0403205317 sf0403200920 4 3205317 1.68E-20 3.82E-07
vg1007453782 sf1007469405 10 7453782 8.29E-18 1.27E-10
vg1007629130 sf1007644739 10 7629130 1.54E-17 8.84E-11
vg0110929029 sf0110928005 1 10929029 1.07E-14 4.98E-06
vg1010635166 sf1010563987 10 10635166 3.67E-14 1.06E-06
vg0710047549 sf0710046555 7 10047549 4.12E-14 2.31E-06
vg1216843191 sf1216837145 12 16843191 1.07E-12 1.30E-06
vg0407826743 sf0407822011 4 7826743 1.82E-12 3.77E-07
vg0222742146 sf0222736277 2 22742146 NA 4.00E-08
vg0222742213 sf0222736344 2 22742213 NA 6.61E-08
vg0223668140 sf0223662271 2 23668140 NA 1.13E-06
vg0818558485 sf0818555772 8 18558485 NA 2.12E-06
vg0813669113 sf0813666399 8 13669113 NA 2.37E-06
Unknow sf1004109164 Unknow Unknow NA 3.00E-06