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 mr1737 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
vg0714864470 sf0714863477 7 14864470 4.84E-34 NA
vg0435460049 sf0435274926 4 35460049 6.14E-34 NA
vg0137817100 sf0137816057 1 37817100 9.13E-34 NA
vg0204214626 sf0204214623 2 4214626 9.34E-34 NA
vg0918001006 sf0918000005 9 18001006 3.16E-33 NA
vg0137911881 sf0137910838 1 37911881 7.46E-33 NA
vg0314756039 sf0314754726 3 14756039 NA 1.35E-06
vg0314727170 sf0314725857 3 14727170 NA 1.37E-06
vg0315366561 sf0315365208 3 15366561 NA 3.12E-06
vg0521861498 sf0521798940 5 21861498 NA 3.39E-06
vg1106746957 sf1106742710 11 6746957 NA 6.79E-06