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 mr1228 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
vg0119055917 sf0119054872 1 19055917 1.14E-18 NA
vg0626673383 sf0626672386 6 26673383 5.31E-18 NA
vg0901694611 sf0901693611 9 1694611 6.59E-18 NA
vg0213899397 sf0213893527 2 13899397 7.73E-18 NA
vg0226005282 sf0225999413 2 26005282 8.36E-18 NA
vg1013414763 sf1013343533 10 13414763 6.36E-17 NA
vg0608469056 sf0608468057 6 8469056 5.59E-16 9.78E-06
vg1215651261 sf1215648558 12 15651261 NA 5.14E-06