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 mr1284 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
vg0709448532 sf0709447538 7 9448532 8.12E-09 8.12E-09
vg0420711795 sf0420539838 4 20711795 5.10E-08 5.10E-08
vg0819484888 sf0819482175 8 19484888 5.78E-08 5.78E-08
vg0805826839 sf0805825842 8 5826839 1.03E-07 1.03E-07
vg0717084739 sf0717083746 7 17084739 1.79E-07 1.79E-07
vg0516885177 sf0516824818 5 16885177 1.82E-07 1.82E-07
vg0704732672 sf0704731673 7 4732672 2.46E-07 2.46E-07
vg0714622950 sf0714621957 7 14622950 6.27E-07 6.27E-07
vg0122971925 sf0122970881 1 22971925 1.57E-06 1.57E-06
vg0410770678 sf0410761379 4 10770678 1.67E-06 1.67E-06
vg0235581681 sf0235575812 2 35581681 2.09E-06 2.09E-06
vg0921004343 sf0921003862 9 21004343 2.56E-06 2.56E-06
vg0709176903 sf0709175909 7 9176903 2.84E-06 2.84E-06
vg0607674962 sf0607673963 6 7674962 4.09E-06 4.09E-06
vg0410534481 sf0410525180 4 10534481 4.15E-06 4.15E-06
vg0407320870 sf0407316140 4 7320870 4.16E-06 4.16E-06
vg1023087868 sf1023016341 10 23087868 4.51E-06 4.51E-06
vg0706405260 sf0706404265 7 6405260 5.36E-06 5.36E-06
vg0607980327 sf0607979328 6 7980327 6.77E-06 6.77E-06