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 mr1090 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
vg0610606146 sf0610605147 6 10606146 3.81E-148 7.51E-60
vg0610608095 sf0610607096 6 10608095 8.88E-148 4.54E-67
vg0611081509 sf0611080510 6 11081509 1.92E-76 1.52E-09
vg0709238656 sf0709237662 7 9238656 2.15E-70 NA
vg0616519927 sf0616518929 6 16519927 2.14E-67 NA
vg0423817901 sf0423632758 4 23817901 2.31E-67 NA
vg0717252215 sf0717251222 7 17252215 2.76E-67 NA
vg0619135527 sf0619134530 6 19135527 2.41E-62 1.53E-07
vg0116412234 sf0116411208 1 16412234 3.00E-59 1.48E-07
vg0610532672 sf0610531673 6 10532672 NA 3.99E-59
vg0610532947 sf0610531948 6 10532947 NA 2.42E-51
vg0610532396 sf0610531397 6 10532396 NA 9.36E-46
vg0610685711 sf0610684712 6 10685711 NA 6.01E-24
vg0610763769 sf0610762770 6 10763769 NA 3.73E-17
vg0610444069 sf0610443070 6 10444069 NA 2.76E-16
vg0610118930 sf0610117931 6 10118930 NA 7.54E-16
vg0610082555 sf0610081556 6 10082555 NA 1.93E-12
vg0610723832 sf0610722833 6 10723832 NA 7.51E-12
vg0611081410 sf0611080411 6 11081410 NA 1.39E-10
vg1208133155 sf1208130561 12 8133155 NA 1.63E-10
vg0610287062 sf0610286063 6 10287062 NA 8.44E-10
vg0610678495 sf0610677496 6 10678495 NA 6.08E-09
vg0108044840 sf0108043840 1 8044840 NA 9.51E-09
vg0609926308 sf0609925309 6 9926308 NA 9.91E-09
vg0206102860 sf0206102860 2 6102860 NA 1.56E-08
vg0610453711 sf0610452712 6 10453711 NA 2.11E-08
vg0609929059 sf0609928060 6 9929059 NA 2.70E-08
vg0304745816 sf0304744818 3 4745816 NA 3.38E-08
vg0610197477 sf0610196478 6 10197477 NA 5.54E-08
vg0434837711 sf0434652602 4 34837711 NA 6.80E-08
vg0615907055 sf0615906057 6 15907055 NA 7.08E-08
vg0610455817 sf0610454818 6 10455817 NA 1.72E-07
vg0610645391 sf0610644392 6 10645391 NA 2.47E-07
vg0611125709 sf0611124710 6 11125709 NA 2.85E-07