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 mr1134 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
vg0138124102 sf0138123059 1 38124102 1.21E-119 1.26E-25
vg0137930974 sf0137929931 1 37930974 2.68E-119 1.37E-30
vg1119431785 sf1118965473 11 19431785 1.33E-93 2.66E-06
vg1014521519 sf1014450285 10 14521519 5.23E-93 5.49E-06
vg0206254749 sf0206254749 2 6254749 6.87E-91 NA
vg0221214821 sf0221208953 2 21214821 1.29E-90 NA
vg0206300800 sf0206300800 2 6300800 7.08E-90 NA
vg1119344402 sf1118878090 11 19344402 1.01E-88 1.26E-06
vg0220998391 sf0220992523 2 20998391 9.81E-88 7.47E-07
vg0232358383 sf0232352514 2 32358383 2.17E-86 2.45E-06
vg1017577102 sf1017505875 10 17577102 1.31E-85 2.30E-06
vg0805845997 sf0805845000 8 5845997 1.76E-85 3.27E-06
vg0205437290 sf0205437290 2 5437290 3.37E-84 2.60E-07
vg1112875793 sf1112412114 11 12875793 2.20E-82 2.41E-06
vg0406043021 sf0406038460 4 6043021 NA 2.59E-08
vg1012912242 sf1012841057 10 12912242 NA 4.23E-08
vg0108147243 sf0108146243 1 8147243 NA 7.67E-08
vg0100095775 sf0100094775 1 95775 NA 1.03E-07
vg0630161553 sf0630160555 6 30161553 NA 1.35E-07
vg0138147992 sf0138146949 1 38147992 NA 2.67E-07
vg1107200695 sf1107196440 11 7200695 NA 3.06E-07
vg0138161446 sf0138160403 1 38161446 NA 3.41E-07
vg0810945945 sf0810944950 8 10945945 NA 7.02E-07
vg0137934558 sf0137933515 1 37934558 NA 8.44E-07
vg1101043468 sf1101042469 11 1043468 NA 9.18E-07
vg0706437051 sf0706436056 7 6437051 NA 1.09E-06
vg0812112372 sf0812111377 8 12112372 NA 1.52E-06
vg0124206667 sf0124205623 1 24206667 NA 1.71E-06
vg0819139306 sf0819136593 8 19139306 NA 1.78E-06
vg1116636322 sf1116171200 11 16636322 NA 2.34E-06
vg0702584931 sf0702583932 7 2584931 NA 2.77E-06