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 mr1835 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
vg1102103286 sf1102099144 11 2103286 2.46E-10 4.80E-07
vg0528032302 sf0527969657 5 28032302 1.45E-09 4.64E-06
vg0528030892 sf0527968247 5 28030892 1.74E-09 4.59E-06
vg1217065594 sf1217059549 12 17065594 1.82E-08 NA
vg1102726033 sf1102721937 11 2726033 1.91E-08 NA
vg0407010552 sf0407005823 4 7010552 8.00E-08 NA
vg0617685840 sf0617684843 6 17685840 2.72E-07 7.82E-06
vg0406706214 sf0406701661 4 6706214 2.80E-07 NA
vg0402467869 sf0402463467 4 2467869 6.71E-07 1.97E-06
vg0402461715 sf0402457313 4 2461715 7.14E-06 1.81E-06
vg1218456407 sf1218427843 12 18456407 NA 9.41E-07
vg1216001878 sf1215999174 12 16001878 NA 2.29E-06