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 mr1487 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
vg1209750232 sf1209747641 12 9750232 2.55E-07 2.55E-07
vg1215159569 sf1215156905 12 15159569 5.62E-07 5.62E-07
vg1011517194 sf1011446013 10 11517194 7.60E-07 7.60E-07
vg0431655631 sf0431470524 4 31655631 9.93E-07 9.93E-07
vg1221859917 sf1221826464 12 21859917 1.32E-06 1.33E-06
vg1217635826 sf1217629781 12 17635826 1.94E-06 1.94E-06
vg1215178307 sf1215175643 12 15178307 2.17E-06 2.17E-06
vg0820000626 sf0819997913 8 20000626 2.84E-06 2.85E-06
vg1221860511 sf1221827058 12 21860511 2.88E-06 2.88E-06
vg0115958705 sf0115957679 1 15958705 3.08E-06 3.08E-06
vg1210198509 sf1210195920 12 10198509 3.80E-06 3.80E-06
vg0431614108 sf0431429003 4 31614108 6.63E-06 6.63E-06