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 mr1895 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
vg0912355268 sf0912354267 9 12355268 6.59E-12 6.82E-06
vg0404546700 sf0404542303 4 4546700 3.57E-10 NA
vg0427380906 sf0427195770 4 27380906 7.25E-10 NA
vg0224678499 sf0224672630 2 24678499 7.66E-10 1.16E-06
vg0916269577 sf0916268576 9 16269577 1.67E-09 NA
vg0427491156 sf0427306019 4 27491156 3.32E-09 NA
vg0907518119 sf0907517119 9 7518119 3.51E-09 NA
vg0911114713 sf0911113712 9 11114713 1.44E-07 2.30E-06
vg0219499870 sf0219494002 2 19499870 4.01E-06 NA