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 mr1896 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
vg0524737028 sf0524674449 5 24737028 6.20E-38 6.99E-25
vg1100512559 sf1100511562 11 512559 5.71E-18 9.83E-08
vg0600846944 sf0600845945 6 846944 3.60E-14 5.36E-06
vg1205231921 sf1205230907 12 5231921 1.21E-13 3.16E-08
vg0601362942 sf0601361943 6 1362942 6.40E-13 3.13E-06
vg1122446629 sf1121980500 11 22446629 7.52E-13 1.49E-07
vg1120734654 sf1120268557 11 20734654 3.14E-11 1.09E-06
vg1117053183 sf1116587035 11 17053183 5.85E-11 4.22E-07
vg1122459168 sf1121993039 11 22459168 4.26E-09 6.45E-08
vg0521749530 sf0521686972 5 21749530 NA 8.13E-07
vg0623976109 sf0623975112 6 23976109 NA 2.95E-06
vg0324099807 sf0324097886 3 24099807 NA 8.01E-06