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 mr1425 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
vg1213458686 sf1213456024 12 13458686 4.79E-14 2.83E-06
vg1208089057 sf1208086463 12 8089057 2.91E-13 NA
vg1213459800 sf1213457138 12 13459800 2.17E-12 6.27E-07
vg0912184179 sf0912183178 9 12184179 1.90E-11 3.60E-06
vg0912195782 sf0912194781 9 12195782 2.61E-11 2.74E-06
vg1218416620 sf1218388056 12 18416620 3.07E-11 NA
vg1208985464 sf1208982872 12 8985464 3.35E-11 5.91E-07
vg0314124501 sf0314123190 3 14124501 5.21E-11 4.48E-06
vg0528501350 sf0528438705 5 28501350 2.83E-10 6.80E-07
vg0726050168 sf0726049174 7 26050168 2.64E-08 6.02E-07
vg1118132551 sf1117666409 11 18132551 2.87E-08 3.43E-07
vg0715369987 sf0715368994 7 15369987 1.06E-06 NA
vg1218169210 sf1218140646 12 18169210 1.07E-06 NA
vg0802263992 sf0802262995 8 2263992 1.47E-06 2.00E-06
vg1126694376 sf1126222763 11 26694376 8.15E-06 NA
vg1208480660 sf1208478067 12 8480660 NA 3.20E-08
vg0407669199 sf0407664466 4 7669199 NA 4.86E-06
vg0821500132 sf0821497419 8 21500132 NA 8.96E-06