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 mr1821 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
vg0719952632 sf0719951639 7 19952632 4.55E-14 3.86E-08
vg1003467337 sf1003466314 10 3467337 1.68E-11 9.26E-06
vg0620904318 sf0620903321 6 20904318 7.21E-11 3.39E-07
vg0313995582 sf0313994299 3 13995582 7.36E-11 NA
vg1216676408 sf1216670362 12 16676408 1.22E-10 7.06E-07
vg1216560675 sf1216557968 12 16560675 3.40E-10 2.30E-07
vg0328780990 sf0328774044 3 28780990 3.41E-10 8.51E-07
vg0529163752 sf0529101107 5 29163752 5.42E-09 3.84E-06
vg0525530135 sf0525467556 5 25530135 8.28E-09 3.66E-06
vg1005877282 sf1005893820 10 5877282 NA 1.99E-06
vg1100882780 sf1100881781 11 882780 NA 4.11E-06