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 mr1009 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 5.72E-36 2.53E-26
vg0133599398 sf0133598354 1 33599398 5.09E-31 2.49E-23
vg0135297102 sf0135296059 1 35297102 2.18E-16 2.36E-13
vg0133643942 sf0133642898 1 33643942 1.33E-14 2.96E-09
vg0133420260 sf0133419216 1 33420260 3.55E-13 7.71E-09
vg0133592451 sf0133591407 1 33592451 2.86E-12 1.20E-07
vg0133432234 sf0133431190 1 33432234 9.42E-12 3.41E-07
vg0901967595 sf0901966595 9 1967595 2.49E-11 4.30E-07
vg0134821080 sf0134820037 1 34821080 8.87E-11 4.36E-07
vg0134673347 sf0134672304 1 34673347 1.17E-10 1.04E-08
vg0900280849 sf0900279849 9 280849 2.43E-10 1.71E-07
vg0133799491 sf0133798447 1 33799491 9.84E-10 2.76E-07
vg0901739357 sf0901738357 9 1739357 2.35E-09 2.32E-07
vg0133266800 sf0133265756 1 33266800 5.81E-09 9.44E-08
vg0134429658 sf0134428615 1 34429658 6.71E-09 2.08E-08
vg0131505553 sf0131504509 1 31505553 6.98E-09 1.83E-07
vg0132257174 sf0132256130 1 32257174 1.08E-08 2.22E-07
vg1010364023 sf1010292844 10 10364023 2.68E-08 9.01E-08
vg0134971015 sf0134969972 1 34971015 6.10E-07 1.10E-07
vg0133305513 sf0133304469 1 33305513 9.05E-07 9.60E-08
vg0133276859 sf0133275815 1 33276859 NA 1.83E-07