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 mr1309 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
vg1125118463 sf1124652303 11 25118463 2.22E-24 7.75E-25
vg1124875808 sf1124409648 11 24875808 4.20E-09 3.56E-11
vg0704638640 sf0704637641 7 4638640 1.24E-08 4.57E-06
vg1124991220 sf1124525060 11 24991220 1.86E-08 3.53E-13
vg0704635310 sf0704634311 7 4635310 2.31E-08 3.04E-06
vg1124914537 sf1124448377 11 24914537 2.74E-07 7.07E-14
vg1124931687 sf1124465527 11 24931687 9.23E-07 2.43E-09
vg1125544208 sf1125078047 11 25544208 1.25E-06 4.27E-06
vg0208396236 sf0208396235 2 8396236 NA 2.18E-07
vg1124998826 sf1124532666 11 24998826 NA 2.71E-07
vg1124908110 sf1124441950 11 24908110 NA 3.37E-06
vg1122501574 sf1122035445 11 22501574 NA 3.67E-06
vg0328637867 sf0328630920 3 28637867 NA 4.77E-06
vg1125162180 sf1124696020 11 25162180 NA 4.93E-06