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 mr1576 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
vg0306345158 sf0306344158 3 6345158 2.36E-13 NA
vg1208031898 sf1208029304 12 8031898 7.51E-13 NA
vg0426777183 sf0426592060 4 26777183 1.83E-12 2.05E-06
vg0140366212 sf0140365169 1 40366212 2.17E-12 NA
vg0503454043 sf0503454020 5 3454043 2.49E-12 NA
vg1115381015 sf1114917327 11 15381015 8.42E-12 4.55E-06
vg0109942704 sf0109941680 1 9942704 3.86E-09 NA
vg0316604658 sf0316603303 3 16604658 1.79E-08 9.32E-07
vg0630306971 sf0630305973 6 30306971 NA 1.00E-06
vg0709128655 sf0709127661 7 9128655 NA 4.68E-06