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
vg1017173737 sf1017102510 10 17173737 7.58E-15 NA
vg1122053907 sf1121587778 11 22053907 3.16E-13 NA
vg0414114780 sf0414105495 4 14114780 3.55E-13 NA
vg0103394422 sf0103393422 1 3394422 6.27E-13 NA
vg0914077841 sf0914076840 9 14077841 8.81E-13 NA
vg0805392000 sf0805391003 8 5392000 1.54E-12 7.48E-06
vg1115817874 sf1115354182 11 15817874 6.85E-11 NA
vg0125130488 sf0125129444 1 25130488 1.06E-10 NA
vg0417960323 sf0417788364 4 17960323 NA 3.99E-06