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 mr1082 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
vg0217141800 sf0217135930 2 17141800 6.70E-14 7.58E-07
vg0216865447 sf0216859577 2 16865447 1.91E-13 1.73E-06
vg0613011415 sf0613010416 6 13011415 2.64E-13 1.29E-07
vg1101084213 sf1101083214 11 1084213 3.30E-12 NA
vg0719001862 sf0719000869 7 19001862 6.48E-12 7.35E-09
vg0719250996 sf0719250003 7 19250996 8.48E-12 3.01E-06
vg0504617447 sf0504617424 5 4617447 8.73E-12 1.74E-08
vg0431777923 sf0431592816 4 31777923 8.93E-12 6.90E-07
vg1210300519 sf1210297932 12 10300519 2.39E-11 2.20E-06
vg1214370012 sf1214367353 12 14370012 2.87E-11 1.01E-06
vg0717376264 sf0717375271 7 17376264 5.71E-11 5.65E-08
vg0228423420 sf0228417551 2 28423420 1.61E-10 2.74E-06
vg0429428460 sf0429243327 4 29428460 1.85E-10 2.72E-07
vg0624956402 sf0624955405 6 24956402 5.42E-10 3.65E-06
vg0613374759 sf0613373760 6 13374759 6.76E-10 1.38E-06
vg0113880001 sf0113878975 1 13880001 1.41E-09 2.11E-06
vg0418072859 sf0417900900 4 18072859 1.64E-09 NA
vg0216784769 sf0216778899 2 16784769 1.92E-09 NA
vg0717317743 sf0717316750 7 17317743 2.06E-09 5.42E-07
vg0721118397 sf0721117404 7 21118397 7.71E-09 9.55E-07
vg0800667883 sf0800666883 8 667883 NA 2.32E-06
vg0427388465 sf0427203329 4 27388465 NA 2.66E-06