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
vg0417121176 sf0416949218 4 17121176 1.29E-25 2.43E-10
vg0417244171 sf0417072212 4 17244171 4.80E-24 7.20E-12
vg0406753488 sf0406748934 4 6753488 3.63E-22 1.06E-08
vg0519939017 sf0519876493 5 19939017 4.48E-21 7.10E-09
vg0211588654 sf0211588650 2 11588654 4.13E-20 1.27E-10
vg0821189139 sf0821186426 8 21189139 3.98E-19 NA
vg0401887481 sf0401883077 4 1887481 7.05E-18 1.32E-07
vg0905685207 sf0905684207 9 5685207 7.33E-18 2.89E-07
vg0817537465 sf0817534751 8 17537465 1.57E-17 4.37E-08
vg0504159174 sf0504159151 5 4159174 3.20E-17 9.82E-07
vg0821086229 sf0821083516 8 21086229 1.82E-16 6.28E-07
vg1013723877 sf1013652646 10 13723877 2.28E-16 1.28E-06
vg0515059058 sf0515001600 5 15059058 6.09E-15 2.91E-07
vg0515087706 sf0515030248 5 15087706 2.94E-14 3.36E-06
vg0518987903 sf0518925387 5 18987903 6.56E-14 2.39E-09
vg0208505848 sf0208505847 2 8505848 1.43E-12 1.33E-09
vg0314131167 sf0314129856 3 14131167 3.81E-12 NA
vg0702355371 sf0702354372 7 2355371 5.01E-12 NA
vg0130700573 sf0130699529 1 30700573 NA 2.68E-08
vg0403205829 sf0403201432 4 3205829 NA 9.73E-08
vg1220761649 sf1220728197 12 20761649 NA 2.29E-07
vg0417064731 sf0416892773 4 17064731 NA 2.59E-07
vg0208319048 sf0208319047 2 8319048 NA 4.46E-07
vg0809927340 sf0809926344 8 9927340 NA 7.46E-07
vg0823460770 sf0823458057 8 23460770 NA 1.05E-06
vg0818511687 sf0818508974 8 18511687 NA 1.08E-06
vg1217945266 sf1217916700 12 17945266 NA 1.18E-06
vg0101880727 sf0101879727 1 1880727 NA 1.29E-06
vg0618992751 sf0618991754 6 18992751 NA 1.32E-06
vg0520636147 sf0520573588 5 20636147 NA 1.73E-06
vg0408292601 sf0408287875 4 8292601 NA 2.14E-06