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 mr1870 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
vg0715857906 sf0715856913 7 15857906 4.30E-13 NA
vg0139847808 sf0139846765 1 39847808 1.13E-11 NA
vg0805568081 sf0805567084 8 5568081 2.43E-11 NA
vg0706245344 sf0706244345 7 6245344 5.35E-11 NA
vg0820602655 sf0820599942 8 20602655 1.37E-10 NA
vg0426020064 sf0425834939 4 26020064 2.82E-07 NA
vg0921456056 sf0921455575 9 21456056 5.13E-07 4.16E-08
vg0106427492 sf0106426492 1 6427492 1.27E-06 NA
vg0216631549 sf0216625679 2 16631549 2.04E-06 1.21E-06
vg1118344153 sf1117878011 11 18344153 3.17E-06 NA
vg1008658227 sf1008587089 10 8658227 4.05E-06 NA
vg1108336629 sf1108331239 11 8336629 NA 2.01E-06
vg1222647123 sf1222613562 12 22647123 NA 2.67E-06