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 mr1163 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
vg0131668403 sf0131667359 1 31668403 2.40E-10 6.26E-06
vg0138625526 sf0138624483 1 38625526 1.18E-09 NA
vg0138613880 sf0138612837 1 38613880 2.15E-09 NA
vg0141763237 sf0141762194 1 41763237 5.40E-09 NA
vg0134886877 sf0134885834 1 34886877 6.25E-09 NA
vg1102576842 sf1102572746 11 2576842 5.97E-08 NA
vg0911767318 sf0911766317 9 11767318 2.73E-06 NA
vg1209593468 sf1209590877 12 9593468 4.86E-06 2.01E-06
vg1208951133 sf1208948541 12 8951133 5.37E-06 2.29E-06
vg0209208522 sf0209208520 2 9208522 NA 5.09E-07
vg0220043147 sf0220037279 2 20043147 NA 6.47E-07
vg1003042576 sf1003041553 10 3042576 NA 1.35E-06