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 mr1872 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
vg0224664602 sf0224658733 2 24664602 6.03E-09 2.03E-06
vg0826172820 sf0826170106 8 26172820 7.76E-09 7.97E-07
vg0224620813 sf0224614944 2 24620813 8.38E-09 5.05E-07
vg0204236989 sf0204236986 2 4236989 9.79E-09 2.87E-07
vg0421282022 sf0421110076 4 21282022 2.92E-08 1.76E-06
vg0234719079 sf0234713210 2 34719079 3.42E-08 7.18E-06
vg0400113914 sf0400112914 4 113914 3.08E-07 NA
vg1218733502 sf1218704937 12 18733502 NA 1.58E-06
vg0314035630 sf0314034319 3 14035630 NA 1.74E-06
vg1119431678 sf1118965366 11 19431678 NA 2.10E-06
vg1105998872 sf1105994624 11 5998872 NA 3.28E-06
vg1004963409 sf1004979946 10 4963409 NA 3.54E-06