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 mr1228 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
vg1216315099 sf1216312395 12 16315099 1.47E-14 NA
vg0228545798 sf0228539929 2 28545798 1.89E-14 NA
vg0800035708 sf0800034708 8 35708 3.27E-14 NA
vg0820038770 sf0820036057 8 20038770 4.29E-14 1.95E-06
vg0720389845 sf0720388852 7 20389845 1.60E-13 NA
vg0103409881 sf0103408881 1 3409881 1.77E-13 4.01E-06
vg1108671225 sf1108665835 11 8671225 1.78E-13 2.61E-06
vg0819998774 sf0819996061 8 19998774 3.72E-13 6.05E-07
vg0310435974 sf0310434890 3 10435974 1.00E-11 4.66E-06
vg1212567284 sf1212564623 12 12567284 1.19E-10 NA
vg1123494495 sf1123028365 11 23494495 NA 4.79E-06
vg0102369472 sf0102368472 1 2369472 NA 6.68E-06