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 mr1409 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
vg1008709315 sf1008638177 10 8709315 5.94E-20 NA
vg1005433754 sf1005450291 10 5433754 1.50E-19 1.44E-06
vg0335000939 sf0334993809 3 35000939 9.41E-19 2.91E-10
vg1010713156 sf1010641977 10 10713156 2.92E-18 4.06E-06
vg0917817618 sf0917816617 9 17817618 2.85E-17 NA
vg0206039894 sf0206039894 2 6039894 3.67E-17 NA
vg0216741216 sf0216735346 2 16741216 4.09E-13 3.46E-08
vg0307904239 sf0307903177 3 7904239 5.56E-13 NA
vg0726127290 sf0726126296 7 26127290 1.26E-12 NA
vg1201968520 sf1201967518 12 1968520 2.91E-11 NA
vg0400362758 sf0400361756 4 362758 NA 7.55E-08
vg1005384319 sf1005400856 10 5384319 NA 1.13E-07
vg0216664283 sf0216658413 2 16664283 NA 1.49E-07
vg0628022404 sf0628021406 6 28022404 NA 2.10E-07
vg0327427154 sf0327420207 3 27427154 NA 2.49E-07
vg0334733010 sf0334725880 3 34733010 NA 7.09E-07
vg0327424324 sf0327417377 3 27424324 NA 8.97E-07
vg0202722002 sf0202722000 2 2722002 NA 1.86E-06
vg0605613230 sf0605612231 6 5613230 NA 3.14E-06
vg0628029397 sf0628028399 6 28029397 NA 4.10E-06