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 mr1301 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
vg0417244171 sf0417072212 4 17244171 2.31E-30 3.77E-11
vg0519939017 sf0519876493 5 19939017 6.32E-27 1.58E-09
vg0406753488 sf0406748934 4 6753488 1.66E-26 1.14E-09
vg0417168943 sf0416996984 4 17168943 8.99E-25 2.75E-12
vg0401797174 sf0401792769 4 1797174 2.68E-24 1.35E-06
vg0211588654 sf0211588650 2 11588654 6.48E-24 2.39E-08
vg0515669145 sf0515611686 5 15669145 1.36E-22 6.42E-07
vg0410681849 sf0410672551 4 10681849 2.42E-22 2.25E-08
vg0401887481 sf0401883077 4 1887481 2.64E-20 1.78E-08
vg0520541556 sf0520478997 5 20541556 6.05E-19 4.52E-09
vg0821086229 sf0821083516 8 21086229 2.20E-17 3.65E-07
vg0130700573 sf0130699529 1 30700573 NA 4.93E-10
vg0228455926 sf0228450057 2 28455926 NA 3.21E-09
vg0101880727 sf0101879727 1 1880727 NA 7.72E-09
vg0816453653 sf0816450939 8 16453653 NA 1.49E-08
vg0724533303 sf0724532309 7 24533303 NA 2.74E-08
vg0100420087 sf0100419087 1 420087 NA 3.54E-08
vg1212579472 sf1212576811 12 12579472 NA 5.41E-08
vg0417064731 sf0416892773 4 17064731 NA 6.62E-08
vg0809694186 sf0809693190 8 9694186 NA 9.21E-08
vg0403205829 sf0403201432 4 3205829 NA 9.33E-08
vg0208464517 sf0208464516 2 8464517 NA 1.07E-07
vg1120155107 sf1119689029 11 20155107 NA 1.36E-07
vg0627547379 sf0627546381 6 27547379 NA 1.50E-07
vg0620065391 sf0620064394 6 20065391 NA 1.51E-07
vg0205631770 sf0205631770 2 5631770 NA 2.03E-07
vg0512386404 sf0512386334 5 12386404 NA 2.40E-07
vg0518963862 sf0518901346 5 18963862 NA 6.70E-07
vg0417123204 sf0416951246 4 17123204 NA 6.95E-07
vg0139060178 sf0139059135 1 39060178 NA 8.30E-07