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 mr1815 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
vg1017231804 sf1017160577 10 17231804 1.67E-07 1.67E-07
vg0109548538 sf0109547514 1 9548538 2.52E-07 2.52E-07
vg0128527936 sf0128526891 1 28527936 3.52E-07 3.52E-07
vg0139382231 sf0139381188 1 39382231 6.73E-07 6.73E-07
vg0413262397 sf0413253107 4 13262397 1.12E-06 1.12E-06
vg1105162548 sf1105158359 11 5162548 1.15E-06 1.15E-06
vg0601801709 sf0601800710 6 1801709 1.18E-06 1.18E-06
vg0140000565 sf0139999522 1 40000565 1.70E-06 1.70E-06
vg1115801379 sf1115337687 11 15801379 2.05E-06 2.05E-06
vg1217533657 sf1217527612 12 17533657 2.28E-06 2.28E-06
vg0217154297 sf0217148427 2 17154297 2.84E-06 2.84E-06
vg0323490253 sf0323488427 3 23490253 3.18E-06 3.19E-06
vg0727624200 sf0727623206 7 27624200 3.73E-06 3.73E-06
vg1006757388 sf1006773011 10 6757388 4.36E-06 4.36E-06
vg0910031361 sf0910030360 9 10031361 4.55E-06 4.55E-06