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 mr1121 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
vg0610566084 sf0610565085 6 10566084 1.58E-117 9.33E-44
vg0610556910 sf0610555911 6 10556910 4.78E-81 7.01E-24
vg0304965334 sf0304964336 3 4965334 4.33E-60 NA
vg0124329780 sf0124328736 1 24329780 5.92E-60 NA
vg0401829657 sf0401825252 4 1829657 8.64E-60 NA
vg0423897544 sf0423712402 4 23897544 7.17E-59 NA
vg0616574004 sf0616573006 6 16574004 2.31E-51 6.94E-07
vg0610532672 sf0610531673 6 10532672 NA 2.41E-21
vg0610763769 sf0610762770 6 10763769 NA 1.79E-15
vg0610444069 sf0610443070 6 10444069 NA 4.36E-13
vg0610813890 sf0610812891 6 10813890 NA 1.39E-10
vg0609929059 sf0609928060 6 9929059 NA 3.05E-10
vg0615907055 sf0615906057 6 15907055 NA 2.01E-09
vg0610134394 sf0610133395 6 10134394 NA 4.35E-09
vg0610685711 sf0610684712 6 10685711 NA 6.26E-09
vg0610478475 sf0610477476 6 10478475 NA 1.99E-08
vg0612257913 sf0612256914 6 12257913 NA 2.75E-08
vg0618930430 sf0618929433 6 18930430 NA 4.23E-08
vg0619171840 sf0619170843 6 19171840 NA 1.12E-07
vg0613339384 sf0613338385 6 13339384 NA 3.28E-07
vg0611125709 sf0611124710 6 11125709 NA 4.30E-07
vg0403922278 sf0403917884 4 3922278 NA 5.24E-07
vg0614543893 sf0614542894 6 14543893 NA 7.17E-07
vg0627150441 sf0627149444 6 27150441 NA 8.71E-07
vg0609896396 sf0609895397 6 9896396 NA 9.75E-07
vg0921539163 sf0921538682 9 21539163 NA 1.24E-06
vg0609225638 sf0609224639 6 9225638 NA 1.47E-06