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 mr1136 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
vg0205678863 sf0205678863 2 5678863 5.55E-66 3.22E-07
vg0405052013 sf0405047452 4 5052013 3.60E-62 1.07E-06
vg0317799860 sf0317798642 3 17799860 4.47E-60 NA
vg0221233083 sf0221227215 2 21233083 1.04E-59 NA
vg0803251090 sf0803250093 8 3251090 2.68E-59 NA
vg0405218184 sf0405213625 4 5218184 5.24E-59 6.91E-08
vg0405008302 sf0405003741 4 5008302 2.61E-58 1.50E-06
vg0817436608 sf0817433894 8 17436608 2.07E-56 7.01E-08
vg0124714564 sf0124713520 1 24714564 2.37E-56 3.41E-09
vg0626827287 sf0626826290 6 26827287 8.56E-55 1.94E-06
vg0814423056 sf0814420342 8 14423056 4.29E-54 NA
vg0205760250 sf0205760250 2 5760250 NA 1.05E-11
vg1215354383 sf1215351681 12 15354383 NA 3.49E-09
vg0623040717 sf0623039720 6 23040717 NA 7.21E-09
vg1104181171 sf1104177073 11 4181171 NA 7.97E-08
vg0919373263 sf0919372853 9 19373263 NA 3.11E-07
vg0630513082 sf0630512084 6 30513082 NA 3.49E-07
vg0205786160 sf0205786160 2 5786160 NA 3.53E-07
vg0122013723 sf0122012678 1 22013723 NA 3.66E-07
vg1217945266 sf1217916700 12 17945266 NA 3.70E-07
vg0405234320 sf0405229761 4 5234320 NA 8.82E-07
vg1215654794 sf1215652091 12 15654794 NA 1.07E-06
vg0500908975 sf0500908958 5 908975 NA 1.18E-06
vg0810881067 sf0810880072 8 10881067 NA 2.05E-06
vg1204785320 sf1204784305 12 4785320 NA 3.06E-06
vg0113686887 sf0113685861 1 13686887 NA 3.23E-06
vg0317957936 sf0317956718 3 17957936 NA 3.33E-06
vg1122934110 sf1122467981 11 22934110 NA 4.14E-06
vg0810847739 sf0810846744 8 10847739 NA 4.16E-06