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 mr1985 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
vg0322883878 sf0322882367 3 22883878 2.79E-08 NA
vg0922506851 sf0922506370 9 22506851 7.29E-08 NA
vg0826636852 sf0826634138 8 26636852 1.76E-07 2.62E-07
vg0142876260 sf0142875216 1 42876260 2.71E-07 6.11E-07
vg0141729211 sf0141728168 1 41729211 8.28E-07 1.57E-06
vg0626349551 sf0626348554 6 26349551 9.34E-07 NA
vg0142247303 sf0142246259 1 42247303 1.14E-06 1.75E-06
vg0141853151 sf0141852108 1 41853151 3.64E-06 NA
vg0431915576 sf0431730471 4 31915576 NA 1.13E-06