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 mr1308 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
vg1215184814 sf1215182150 12 15184814 1.08E-08 1.65E-06
vg0906569622 sf0906568622 9 6569622 5.28E-08 NA
vg1214204528 sf1214201868 12 14204528 5.45E-08 NA
vg0506620144 sf0506620085 5 6620144 6.41E-08 NA
vg1217759461 sf1217730895 12 17759461 1.67E-07 2.99E-06
vg0216383410 sf0216377540 2 16383410 4.33E-07 2.36E-06
vg1220367571 sf1220339013 12 20367571 4.74E-06 NA
vg0200409865 sf0200409865 2 409865 9.21E-06 NA
vg0802790437 sf0802789440 8 2790437 NA 1.31E-06
vg1219382346 sf1219353816 12 19382346 NA 1.36E-06
vg0121399989 sf0121398944 1 21399989 NA 4.06E-06