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 mr1678 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
vg0200743118 sf0200743118 2 743118 2.19E-08 4.29E-06
vg0200805927 sf0200805927 2 805927 3.28E-07 1.93E-06
vg0310177475 sf0310176391 3 10177475 5.08E-06 3.06E-06
vg1214022772 sf1214020112 12 14022772 7.18E-06 4.20E-07
vg0122431924 sf0122430879 1 22431924 8.26E-06 NA
vg0506745303 sf0506745245 5 6745303 NA 5.82E-07
vg0711961663 sf0711960669 7 11961663 NA 2.02E-06