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 mr1902 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
vg0724490482 sf0724489488 7 24490482 4.10E-62 1.68E-50
vg0724516475 sf0724515481 7 24516475 5.70E-62 2.75E-50
vg0331232428 sf0331225313 3 31232428 8.43E-32 8.38E-10
vg0331273100 sf0331265985 3 31273100 1.92E-31 5.61E-10
vg0331303645 sf0331296530 3 31303645 2.56E-31 2.45E-10
vg0103583289 sf0103582289 1 3583289 2.93E-23 1.36E-06
vg0102349632 sf0102348632 1 2349632 3.12E-23 2.56E-08
vg0801629578 sf0801628580 8 1629578 1.08E-22 7.77E-06
vg1117638540 sf1117172396 11 17638540 1.78E-22 7.73E-06
vg1000389182 sf1000388182 10 389182 1.26E-21 1.64E-10
vg0723183493 sf0723182500 7 23183493 1.03E-20 1.10E-08
vg1117531985 sf1117065840 11 17531985 1.22E-19 5.63E-10
vg0400999452 sf0400995004 4 999452 5.88E-19 2.30E-09
vg0133286262 sf0133285218 1 33286262 2.95E-18 NA
vg0210489813 sf0210489811 2 10489813 2.87E-17 1.26E-07
vg0725312603 sf0725311609 7 25312603 9.91E-17 1.05E-11
vg0800814630 sf0800813632 8 814630 6.03E-16 6.47E-10
vg0724633083 sf0724632089 7 24633083 5.21E-15 6.42E-08
vg0724513486 sf0724512492 7 24513486 NA 1.12E-30
vg0724401667 sf0724400673 7 24401667 NA 3.38E-19
vg0724477402 sf0724476408 7 24477402 NA 6.14E-17
vg0724510628 sf0724509634 7 24510628 NA 1.62E-15
vg0724381738 sf0724380744 7 24381738 NA 1.13E-12
vg0233123079 sf0233117210 2 33123079 NA 1.27E-09
vg0101034362 sf0101033362 1 1034362 NA 1.30E-09
vg1201219940 sf1201218940 12 1219940 NA 1.99E-09
vg0723574000 sf0723573007 7 23574000 NA 3.63E-09
vg0725053273 sf0725052279 7 25053273 NA 9.77E-09
vg0724522889 sf0724521895 7 24522889 NA 2.57E-08
vg1106630123 sf1106625876 11 6630123 NA 1.61E-06