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 mr1410 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
vg0417238354 sf0417066395 4 17238354 2.80E-43 4.73E-29
vg0519939017 sf0519876493 5 19939017 7.05E-31 2.51E-19
vg0403055424 sf0403051028 4 3055424 1.48E-27 4.79E-15
vg0406753488 sf0406748934 4 6753488 2.61E-26 1.74E-12
vg0211588654 sf0211588650 2 11588654 1.71E-25 9.35E-17
vg0905391874 sf0905390874 9 5391874 3.87E-24 4.30E-12
vg0309190281 sf0309189217 3 9190281 1.16E-23 1.33E-10
vg0111490485 sf0111489461 1 11490485 8.77E-23 1.76E-10
vg0614236515 sf0614235516 6 14236515 1.45E-22 2.93E-10
vg0823849578 sf0823846864 8 23849578 1.57E-22 1.04E-09
vg0902627466 sf0902626466 9 2627466 3.38E-22 9.44E-10
vg0817661668 sf0817658955 8 17661668 4.51E-22 4.88E-13
vg0413423284 sf0413413998 4 13423284 6.65E-22 9.31E-10
vg0718615443 sf0718614450 7 18615443 7.37E-22 3.94E-10
vg0410681849 sf0410672551 4 10681849 1.10E-20 8.28E-11
vg1013723877 sf1013652646 10 13723877 5.72E-19 5.77E-10
vg0728820356 sf0728819364 7 28820356 1.09E-18 5.55E-10
vg0821047605 sf0821044892 8 21047605 1.97E-18 7.15E-12
vg0821141087 sf0821138374 8 21141087 2.08E-18 8.71E-13
vg0718641746 sf0718640753 7 18641746 1.75E-14 3.96E-10
vg0518987917 sf0518925401 5 18987917 3.76E-14 3.65E-13
vg0816724411 sf0816721697 8 16724411 NA 1.42E-07
vg0112473941 sf0112472915 1 12473941 NA 9.82E-06