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 mr1841 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
vg1124335549 sf1123869393 11 24335549 1.97E-16 1.72E-13
vg0812486826 sf0812485730 8 12486826 6.55E-15 3.88E-11
vg0620312022 sf0620311025 6 20312022 9.52E-13 3.00E-08
vg1124965681 sf1124499521 11 24965681 1.74E-12 2.12E-12
vg0713136981 sf0713135988 7 13136981 4.85E-11 1.42E-07
vg0407782510 sf0407777778 4 7782510 7.88E-11 3.27E-07
vg0805901665 sf0805900668 8 5901665 9.29E-11 3.58E-07
vg0113026938 sf0113025912 1 13026938 1.80E-10 2.73E-08
vg1104422127 sf1104418029 11 4422127 3.20E-10 1.87E-08
vg0410375848 sf0410366547 4 10375848 3.45E-10 9.28E-07
vg0815665575 sf0815662861 8 15665575 2.05E-09 3.83E-07
vg0525249866 sf0525187287 5 25249866 2.88E-09 1.80E-06
vg1125316910 sf1124850750 11 25316910 1.49E-08 2.00E-07
vg0301969630 sf0301968626 3 1969630 1.55E-08 4.26E-06
vg0601001133 sf0601000134 6 1001133 2.38E-08 1.95E-07
vg0521578860 sf0521511524 5 21578860 3.28E-08 1.02E-06
vg1126219428 sf1125747842 11 26219428 2.69E-07 1.56E-06
vg0921997124 sf0921996643 9 21997124 5.00E-07 2.60E-06
vg0520747897 sf0520685338 5 20747897 6.15E-07 6.25E-07
vg0715539794 sf0715538801 7 15539794 7.68E-07 8.89E-08