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 mr1457 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
vg1218514358 sf1218485794 12 18514358 3.78E-21 5.67E-10
vg1218595780 sf1218567216 12 18595780 7.79E-21 2.57E-10
vg1218595627 sf1218567063 12 18595627 2.14E-20 3.51E-10
vg1204434963 sf1204433951 12 4434963 2.16E-15 5.58E-06
vg1109870254 sf1109864831 11 9870254 3.89E-14 2.08E-07
vg1219837830 sf1219809300 12 19837830 1.32E-13 5.22E-07
vg0715907834 sf0715906841 7 15907834 3.39E-13 NA
vg1204159174 sf1204158162 12 4159174 6.18E-13 9.96E-07
vg0103997397 sf0103996397 1 3997397 5.09E-12 4.99E-06
vg1104411559 sf1104407461 11 4411559 NA 3.70E-07
vg1218592189 sf1218563625 12 18592189 NA 6.04E-07
vg1218493508 sf1218464944 12 18493508 NA 1.84E-06
vg0419763973 sf0419592008 4 19763973 NA 2.82E-06
vg0330512598 sf0330505487 3 30512598 NA 3.80E-06
vg1220235213 sf1220206655 12 20235213 NA 4.77E-06