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 mr1739 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
vg0802210939 sf0802209942 8 2210939 9.97E-68 3.84E-46
vg0802210642 sf0802209645 8 2210642 1.39E-67 3.65E-46
vg0802212244 sf0802211247 8 2212244 1.41E-30 3.58E-38
vg0801799117 sf0801798120 8 1799117 5.93E-25 9.39E-10
vg0721842233 sf0721841240 7 21842233 3.03E-19 NA
vg0801802005 sf0801801008 8 1802005 5.84E-19 5.36E-06
vg0802112147 sf0802111150 8 2112147 9.55E-19 1.30E-07
vg0801958097 sf0801957100 8 1958097 9.61E-18 1.63E-06
vg0702825530 sf0702824531 7 2825530 4.00E-11 3.36E-06
vg1214465724 sf1214463065 12 14465724 NA 2.04E-06
vg1214083827 sf1214081167 12 14083827 NA 2.75E-06
vg0801845030 sf0801844033 8 1845030 NA 3.25E-06
vg0432523372 sf0432338264 4 32523372 NA 3.54E-06
vg0432523363 sf0432338255 4 32523363 NA 3.81E-06
vg0120024869 sf0120023824 1 20024869 NA 4.08E-06