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 mr1812 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
vg0420711795 sf0420539838 4 20711795 2.71E-09 2.71E-09
vg0819484888 sf0819482175 8 19484888 1.40E-08 1.40E-08
vg0122971925 sf0122970881 1 22971925 9.40E-08 9.41E-08
vg0620734924 sf0620733927 6 20734924 3.08E-07 3.08E-07
vg0717084739 sf0717083746 7 17084739 4.19E-07 4.20E-07
vg0424181194 sf0423996055 4 24181194 4.65E-07 4.65E-07
vg0235581681 sf0235575812 2 35581681 5.89E-07 5.90E-07
vg0421287659 sf0421115713 4 21287659 6.10E-07 6.11E-07
vg0409924694 sf0409915392 4 9924694 6.74E-07 6.74E-07
vg0706405260 sf0706404265 7 6405260 8.61E-07 8.61E-07
vg0826110394 sf0826107680 8 26110394 1.77E-06 1.77E-06
vg0805826839 sf0805825842 8 5826839 1.91E-06 1.91E-06
vg1104467562 sf1104463464 11 4467562 1.93E-06 1.93E-06
vg0407320870 sf0407316140 4 7320870 2.09E-06 2.09E-06
vg0516508609 sf0516451091 5 16508609 2.26E-06 2.26E-06
vg0616107808 sf0616106810 6 16107808 2.65E-06 2.65E-06
vg0623981969 sf0623980972 6 23981969 2.81E-06 2.81E-06
vg0921004343 sf0921003862 9 21004343 2.92E-06 2.92E-06
vg1104063322 sf1104059224 11 4063322 3.11E-06 3.11E-06
vg0131779655 sf0131778611 1 31779655 3.24E-06 3.24E-06
vg1215307750 sf1215305048 12 15307750 3.95E-06 3.95E-06