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 mr1008 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
vg0133244665 sf0133243621 1 33244665 4.38E-37 3.66E-26
vg0133596937 sf0133595893 1 33596937 1.12E-32 5.35E-25
vg0135297102 sf0135296059 1 35297102 1.26E-15 9.88E-12
vg0133643942 sf0133642898 1 33643942 3.23E-15 2.36E-09
vg0133420260 sf0133419216 1 33420260 1.61E-13 1.09E-08
vg0133432234 sf0133431190 1 33432234 7.15E-12 4.90E-07
vg0133592451 sf0133591407 1 33592451 8.55E-12 4.23E-07
vg0134351900 sf0134350857 1 34351900 6.69E-11 5.08E-08
vg0134673347 sf0134672304 1 34673347 1.61E-10 2.42E-08
vg0133266800 sf0133265756 1 33266800 8.08E-10 2.34E-08
vg0134429658 sf0134428615 1 34429658 2.17E-09 4.37E-09
vg0131505553 sf0131504509 1 31505553 6.60E-09 3.01E-07
vg0901739357 sf0901738357 9 1739357 6.97E-09 9.66E-07
vg0900280526 sf0900279526 9 280526 1.27E-08 1.78E-07
vg0132257174 sf0132256130 1 32257174 1.58E-08 3.28E-07
vg1010364023 sf1010292844 10 10364023 6.85E-08 2.54E-07
vg0134971015 sf0134969972 1 34971015 1.44E-07 2.70E-07
vg0404020580 sf0404016187 4 4020580 2.91E-07 3.10E-07
vg0133305513 sf0133304469 1 33305513 8.20E-07 1.80E-08
vg0403542499 sf0403538103 4 3542499 3.39E-06 NA
vg1015010372 sf1014939138 10 15010372 5.61E-06 1.64E-06
vg0920463612 sf0920463131 9 20463612 5.88E-06 4.65E-07
vg0133276859 sf0133275815 1 33276859 NA 3.99E-08