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 mr1836 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
vg0817612440 sf0817609727 8 17612440 3.00E-16 1.15E-10
vg0817611509 sf0817608796 8 17611509 7.10E-16 4.60E-11
vg0818186823 sf0818184110 8 18186823 6.30E-14 7.17E-12
vg0818718847 sf0818716134 8 18718847 1.19E-11 1.68E-07
vg0707392578 sf0707391583 7 7392578 4.51E-10 NA
vg0908710872 sf0908709871 9 8710872 5.54E-10 NA
vg0908639557 sf0908638556 9 8639557 5.99E-10 4.31E-06
vg0129625707 sf0129624662 1 29625707 1.30E-09 NA
vg0818343822 sf0818341109 8 18343822 1.99E-09 8.94E-08
vg0121492519 sf0121491474 1 21492519 3.17E-09 NA
vg0817551415 sf0817548701 8 17551415 9.79E-09 1.51E-06
vg0817362014 sf0817359300 8 17362014 1.23E-08 8.57E-07
vg0922079736 sf0922079255 9 22079736 2.75E-08 NA
vg1116386156 sf1115921033 11 16386156 4.00E-08 2.76E-06
vg0817557170 sf0817554456 8 17557170 1.43E-07 2.97E-06
vg0817619778 sf0817617065 8 17619778 3.68E-07 1.32E-06
vg1011510153 sf1011438972 10 11510153 3.87E-07 NA
vg0817662622 sf0817659909 8 17662622 NA 1.88E-08
vg1202342821 sf1202341822 12 2342821 NA 8.41E-08
vg0320620607 sf0320619117 3 20620607 NA 1.39E-06
vg0828407010 sf0828399490 8 28407010 NA 4.68E-06