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 mr1536 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
vg0614224943 sf0614223944 6 14224943 2.73E-82 1.45E-08
vg0616637848 sf0616636850 6 16637848 3.00E-79 4.80E-12
vg0616788939 sf0616787941 6 16788939 3.83E-79 5.68E-08
vg0614107939 sf0614106940 6 14107939 1.12E-78 6.49E-13
vg0619515677 sf0619514680 6 19515677 1.32E-77 NA
vg0619681040 sf0619680043 6 19681040 9.46E-76 2.54E-07
vg0213031762 sf0213031758 2 13031762 5.01E-75 NA
vg0716925293 sf0716924300 7 16925293 9.04E-75 NA
vg0211839911 sf0211839907 2 11839911 9.74E-73 3.81E-06
vg0133408824 sf0133407780 1 33408824 2.41E-72 1.47E-06
vg0619441061 sf0619440064 6 19441061 1.36E-71 3.48E-08
vg0921471036 sf0921470555 9 21471036 NA 6.37E-09
vg0921425514 sf0921425033 9 21425514 NA 1.06E-08
vg0613449469 sf0613448470 6 13449469 NA 8.91E-07
vg0921465189 sf0921464708 9 21465189 NA 2.60E-06
vg1217551780 sf1217545735 12 17551780 NA 2.65E-06
vg1218237165 sf1218208601 12 18237165 NA 3.00E-06
vg0717004704 sf0717003711 7 17004704 NA 4.48E-06
vg0133426540 sf0133425496 1 33426540 NA 4.56E-06
vg1213328042 sf1213325380 12 13328042 NA 7.36E-06