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 mr1246 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
vg0719011406 sf0719010413 7 19011406 8.11E-36 3.78E-26
vg0717197101 sf0717196108 7 17197101 6.41E-15 4.86E-11
vg0718887161 sf0718886168 7 18887161 1.38E-13 2.53E-10
vg0719453082 sf0719452089 7 19453082 1.26E-11 NA
vg0719346699 sf0719345706 7 19346699 2.72E-11 3.19E-06
vg0719120113 sf0719119120 7 19120113 2.06E-10 3.35E-06
vg0235249589 sf0235243720 2 35249589 9.15E-10 6.79E-07
vg0719443406 sf0719442413 7 19443406 1.98E-09 3.31E-08
vg0725803058 sf0725802064 7 25803058 3.24E-09 3.69E-06
vg1214119394 sf1214116734 12 14119394 9.69E-09 3.04E-06
vg0305293070 sf0305292070 3 5293070 2.59E-08 1.93E-06
vg0719139080 sf0719138087 7 19139080 2.93E-08 9.75E-07
vg0705751437 sf0705750438 7 5751437 3.15E-08 1.82E-06
vg0827210810 sf0827208096 8 27210810 7.16E-08 3.35E-08
vg0139656695 sf0139655652 1 39656695 1.10E-07 2.34E-07
vg0228211068 sf0228205199 2 28211068 1.19E-06 7.99E-07
vg0821781292 sf0821778579 8 21781292 1.42E-06 8.23E-07
vg1116237651 sf1115772521 11 16237651 2.10E-06 NA
vg1108345384 sf1108339994 11 8345384 7.52E-06 2.55E-06
vg0718985745 sf0718984752 7 18985745 NA 5.53E-09
vg0325679193 sf0325677211 3 25679193 NA 1.47E-06
vg0109413154 sf0109412130 1 9413154 NA 2.01E-06
vg1113441316 sf1112977638 11 13441316 NA 6.81E-06