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 mr1123 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
vg0222726563 sf0222720694 2 22726563 1.23E-15 1.45E-12
vg0222743508 sf0222737639 2 22743508 1.79E-14 3.93E-11
vg0222743520 sf0222737651 2 22743520 1.67E-09 2.19E-06
vg0122405293 sf0122404248 1 22405293 1.28E-08 NA
vg1006839627 sf1006855250 10 6839627 1.40E-08 NA
vg1009538373 sf1009467194 10 9538373 7.42E-08 NA
vg0223976143 sf0223970274 2 23976143 8.64E-08 7.73E-06
vg1124745257 sf1124279097 11 24745257 1.20E-07 1.48E-07
vg0224013851 sf0224007982 2 24013851 1.47E-07 1.04E-06
vg1220410178 sf1220381620 12 20410178 8.04E-06 NA
vg0914798554 sf0914797553 9 14798554 NA 4.37E-06
vg0714200726 sf0714199733 7 14200726 NA 7.72E-06