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 mr1087 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
vg0610608211 sf0610607212 6 10608211 2.74E-137 1.18E-51
vg0610606146 sf0610605147 6 10606146 5.25E-136 7.19E-51
vg0610608095 sf0610607096 6 10608095 2.01E-127 1.74E-52
vg0705560234 sf0705559235 7 5560234 3.90E-80 NA
vg0616950705 sf0616949708 6 16950705 1.75E-79 6.10E-06
vg0310442654 sf0310441570 3 10442654 1.88E-78 NA
vg0617821393 sf0617820396 6 17821393 2.15E-78 8.24E-09
vg0802245269 sf0802244272 8 2245269 4.51E-78 NA
vg0613048915 sf0613047916 6 13048915 3.16E-74 3.27E-06
vg0610678495 sf0610677496 6 10678495 1.04E-71 1.90E-23
vg0610679715 sf0610678716 6 10679715 NA 5.56E-36
vg0610470847 sf0610469848 6 10470847 NA 6.22E-26
vg0610763769 sf0610762770 6 10763769 NA 2.74E-18
vg0610443927 sf0610442928 6 10443927 NA 6.49E-16
vg0610134394 sf0610133395 6 10134394 NA 2.28E-14
vg0610152420 sf0610151421 6 10152420 NA 1.07E-13
vg0610532672 sf0610531673 6 10532672 NA 6.91E-13
vg0611125709 sf0611124710 6 11125709 NA 3.90E-12
vg0610722873 sf0610721874 6 10722873 NA 7.03E-12
vg0611127099 sf0611126100 6 11127099 NA 5.80E-11
vg0609225907 sf0609224908 6 9225907 NA 1.62E-10
vg0610776489 sf0610775490 6 10776489 NA 3.79E-10
vg0610881038 sf0610880039 6 10881038 NA 5.54E-10
vg0610634160 sf0610633161 6 10634160 NA 1.01E-09
vg0609929059 sf0609928060 6 9929059 NA 2.02E-09
vg0611682950 sf0611681951 6 11682950 NA 2.79E-09
vg0610881350 sf0610880351 6 10881350 NA 2.03E-08
vg0611650489 sf0611649490 6 11650489 NA 4.14E-08
vg0222318703 sf0222312834 2 22318703 NA 1.06E-07
vg0613294536 sf0613293537 6 13294536 NA 2.38E-07
vg0610438538 sf0610437539 6 10438538 NA 2.68E-07
vg0222307984 sf0222302115 2 22307984 NA 4.61E-07