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 mr1539 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
vg0129921541 sf0129920496 1 29921541 3.58E-15 1.93E-07
vg1117272721 sf1116806573 11 17272721 3.72E-15 NA
vg1000839305 sf1000838281 10 839305 3.72E-15 NA
vg0520082492 sf0520019968 5 20082492 5.19E-15 5.36E-06
vg0122975265 sf0122974221 1 22975265 1.36E-14 NA
vg0232390959 sf0232385090 2 32390959 8.41E-13 2.98E-06
vg0129868849 sf0129867804 1 29868849 1.52E-12 7.06E-07
vg0314829204 sf0314827851 3 14829204 4.29E-12 1.57E-06
vg0805428634 sf0805427637 8 5428634 4.99E-12 4.05E-06
vg1104181171 sf1104177073 11 4181171 5.73E-12 6.61E-08
vg1122054525 sf1121588396 11 22054525 2.79E-11 2.46E-07
vg1121939386 sf1121473257 11 21939386 5.31E-11 2.64E-07
vg1000735141 sf1000734117 10 735141 1.03E-09 1.88E-06
vg1017103748 sf1017032520 10 17103748 3.68E-09 5.51E-07
vg0411585719 sf0411576423 4 11585719 NA 8.10E-07