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 mr1199 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
vg0719136412 sf0719135419 7 19136412 1.84E-09 1.78E-07
vg0718989547 sf0718988554 7 18989547 5.41E-09 1.44E-07
vg0719209499 sf0719208506 7 19209499 5.58E-09 2.83E-08
vg0519106763 sf0519044247 5 19106763 6.31E-09 NA
vg0304931155 sf0304930157 3 4931155 8.25E-09 3.02E-07
vg0719140447 sf0719139454 7 19140447 2.02E-08 2.55E-07
vg1101783832 sf1101782833 11 1783832 6.17E-08 NA
vg0123309862 sf0123308818 1 23309862 1.12E-07 1.73E-06
vg1202102394 sf1202101392 12 2102394 1.17E-07 3.04E-07
vg1124078478 sf1123612348 11 24078478 3.16E-07 1.10E-07
vg0525073369 sf0525010784 5 25073369 4.91E-06 NA
vg0319282672 sf0319281432 3 19282672 5.19E-06 1.42E-06
vg1016429449 sf1016358223 10 16429449 NA 6.81E-06