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 mr1962 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
vg0406420586 sf0406416026 4 6420586 9.46E-157 5.99E-20
vg0406465683 sf0406461126 4 6465683 9.93E-153 8.77E-23
vg0406526555 sf0406521998 4 6526555 3.10E-151 4.39E-19
vg0307375905 sf0307374903 3 7375905 3.48E-135 NA
vg0412427420 sf0412418134 4 12427420 6.97E-135 NA
vg0718812067 sf0718811074 7 18812067 6.87E-134 NA
vg0705319765 sf0705318766 7 5319765 3.71E-131 NA
vg0222719698 sf0222713829 2 22719698 NA 3.73E-35
vg0222743387 sf0222737518 2 22743387 NA 1.58E-27
vg0222573327 sf0222567458 2 22573327 NA 2.62E-11
vg0406521772 sf0406517215 4 6521772 NA 1.56E-09
vg0222729853 sf0222723984 2 22729853 NA 1.71E-08
vg0407565723 sf0407560992 4 7565723 NA 4.00E-08
vg0223169891 sf0223164022 2 23169891 NA 1.04E-07
vg0507079626 sf0507079568 5 7079626 NA 1.93E-07
vg0406209150 sf0406204590 4 6209150 NA 3.23E-07
vg0224529885 sf0224524016 2 24529885 NA 3.81E-07
vg0223674836 sf0223668967 2 23674836 NA 9.26E-07
vg0406345525 sf0406340965 4 6345525 NA 1.71E-06
vg0209234819 sf0209234817 2 9234819 NA 2.25E-06
vg1011859779 sf1011788594 10 11859779 NA 2.93E-06
vg1003006014 sf1003004991 10 3006014 NA 3.62E-06
vg0514548093 sf0514490636 5 14548093 NA 3.88E-06
vg0313740300 sf0313739017 3 13740300 NA 3.90E-06
vg0223051444 sf0223045575 2 23051444 NA 4.39E-06
vg0406536293 sf0406531736 4 6536293 NA 4.53E-06
vg0313656815 sf0313655532 3 13656815 NA 4.66E-06