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 mr1144 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
vg0610608095 sf0610607096 6 10608095 8.15E-51 3.21E-32
vg0610435285 sf0610434286 6 10435285 6.73E-15 1.08E-11
vg0920307704 sf0920307223 9 20307704 3.53E-14 NA
vg0610419183 sf0610418184 6 10419183 4.89E-14 2.07E-14
vg0610433780 sf0610432781 6 10433780 6.36E-14 8.67E-12
vg0611457307 sf0611456308 6 11457307 4.88E-13 5.05E-07
vg0610684751 sf0610683752 6 10684751 8.44E-13 5.36E-08
vg0616119655 sf0616118657 6 16119655 4.57E-12 8.55E-07
vg0611999588 sf0611998589 6 11999588 9.44E-12 3.31E-07
vg0612051434 sf0612050435 6 12051434 2.12E-11 9.93E-08
vg0611471474 sf0611470475 6 11471474 4.54E-11 3.20E-08
vg0610628699 sf0610627700 6 10628699 9.59E-11 3.97E-09
vg0611096080 sf0611095081 6 11096080 2.05E-10 2.95E-10
vg0610455817 sf0610454818 6 10455817 2.28E-10 2.02E-07
vg0610687475 sf0610686476 6 10687475 8.31E-10 2.75E-10
vg0611119125 sf0611118126 6 11119125 1.72E-09 1.27E-06
vg0614543893 sf0614542894 6 14543893 2.87E-09 5.78E-07
vg0610752667 sf0610751668 6 10752667 3.00E-09 3.57E-12
vg0613063810 sf0613062811 6 13063810 5.81E-09 1.33E-06
vg0610556004 sf0610555005 6 10556004 1.79E-08 6.41E-07
vg0611643367 sf0611642368 6 11643367 3.10E-07 8.74E-07
vg1116906179 sf1116441058 11 16906179 7.31E-07 2.15E-07
vg0610778195 sf0610777196 6 10778195 NA 3.14E-08
vg0617603352 sf0617602355 6 17603352 NA 2.49E-07