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 mr1955 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
vg0601870518 sf0601869519 6 1870518 8.61E-08 8.62E-08
vg0705521102 sf0705520103 7 5521102 2.51E-07 2.51E-07
vg1218885831 sf1218857266 12 18885831 5.47E-07 5.47E-07
vg0705345844 sf0705344845 7 5345844 5.58E-07 5.58E-07
vg0400436154 sf0400435152 4 436154 1.08E-06 1.08E-06
vg0314687749 sf0314686436 3 14687749 2.32E-06 2.32E-06
vg0600092313 sf0600091313 6 92313 2.44E-06 2.44E-06
vg0220496398 sf0220490530 2 20496398 2.99E-06 3.00E-06
vg0434644596 sf0434459486 4 34644596 3.20E-06 3.20E-06
vg0233648723 sf0233642854 2 33648723 3.82E-06 3.82E-06
vg0302286904 sf0302285900 3 2286904 4.91E-06 4.91E-06