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 mr1422 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
vg0719081486 sf0719080493 7 19081486 4.65E-36 NA
vg0610087521 sf0610086522 6 10087521 7.49E-36 7.49E-09
vg0610429989 sf0610428990 6 10429989 1.40E-33 2.03E-10
vg0128158748 sf0128157704 1 28158748 8.91E-32 NA
vg0107088884 sf0107087884 1 7088884 2.99E-31 NA
vg0820939094 sf0820936381 8 20939094 3.57E-31 NA
vg0616930764 sf0616929767 6 16930764 NA 1.52E-08
vg0610212566 sf0610211567 6 10212566 NA 8.90E-08
vg0611735326 sf0611734327 6 11735326 NA 3.18E-07
vg1215582510 sf1215579807 12 15582510 NA 1.06E-06
vg0728892745 sf0728891753 7 28892745 NA 1.46E-06
vg1208634025 sf1208631432 12 8634025 NA 1.89E-06
vg0610102626 sf0610101627 6 10102626 NA 2.28E-06
vg1214981537 sf1214978879 12 14981537 NA 3.43E-06
vg0805970126 sf0805969129 8 5970126 NA 3.49E-06
vg0610788671 sf0610787672 6 10788671 NA 3.78E-06
vg0401505122 sf0401500672 4 1505122 NA 4.43E-06
vg1219575203 sf1219546673 12 19575203 NA 8.01E-06