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 mr1310 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
vg1000442554 sf1000441530 10 442554 1.18E-74 9.75E-34
vg1011110286 sf1011039106 10 11110286 4.44E-45 3.53E-09
vg1011087195 sf1011016015 10 11087195 3.31E-44 6.81E-10
vg1007820831 sf1007836441 10 7820831 8.15E-43 7.95E-08
vg1004324027 sf1004340565 10 4324027 3.84E-41 3.64E-06
vg0700359527 sf0700358527 7 359527 2.14E-40 3.38E-11
vg1008207053 sf1008135915 10 8207053 1.23E-39 1.62E-10
vg1004261816 sf1004278354 10 4261816 1.14E-38 1.36E-07
vg0528146502 sf0528083857 5 28146502 3.95E-37 2.26E-11
vg1125104499 sf1124638339 11 25104499 2.90E-35 1.39E-10
vg1125090609 sf1124624449 11 25090609 NA 3.19E-18
vg0328227704 sf0328220758 3 28227704 NA 9.17E-10
vg1001020612 sf1001019588 10 1020612 NA 1.85E-09
vg0528104538 sf0528041893 5 28104538 NA 3.78E-09
vg0210660828 sf0210660826 2 10660828 NA 4.67E-09
vg1200246210 sf1200245210 12 246210 NA 1.01E-08
vg0402461396 sf0402456994 4 2461396 NA 2.33E-08
vg0129913271 sf0129912226 1 29913271 NA 2.51E-08
vg1122626801 sf1122160672 11 22626801 NA 3.28E-08
vg1200149931 sf1200148931 12 149931 NA 3.38E-08
vg0607242294 sf0607241295 6 7242294 NA 3.44E-08
vg0307980063 sf0307979001 3 7980063 NA 3.88E-08
vg1128791293 sf1128268072 11 28791293 NA 4.02E-08
vg0330670598 sf0330663485 3 30670598 NA 5.26E-08
vg1004777581 sf1004794118 10 4777581 NA 6.10E-08
vg1200323344 sf1200322344 12 323344 NA 6.75E-08
vg0129913679 sf0129912634 1 29913679 NA 1.25E-07
vg1000754147 sf1000753123 10 754147 NA 1.31E-07
vg0103508890 sf0103507890 1 3508890 NA 1.56E-07
vg1000958635 sf1000957611 10 958635 NA 2.04E-07