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 mr1417 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
vg1212214384 sf1212211722 12 12214384 1.54E-07 1.54E-07
vg0200741581 sf0200741581 2 741581 2.25E-07 2.25E-07
vg1006612280 sf1006627903 10 6612280 2.84E-07 2.84E-07
vg1215548475 sf1215545772 12 15548475 3.14E-07 3.14E-07
vg1211121901 sf1211119265 12 11121901 5.50E-07 5.50E-07
vg1216247174 sf1216244470 12 16247174 9.17E-07 9.17E-07
vg0818521526 sf0818518813 8 18521526 1.49E-06 1.49E-06
vg0102539858 sf0102538858 1 2539858 2.07E-06 2.07E-06
vg1128667909 sf1128144688 11 28667909 3.97E-06 3.97E-06
vg0127482594 sf0127481550 1 27482594 4.30E-06 4.30E-06
vg1002115213 sf1002114190 10 2115213 4.59E-06 4.59E-06
vg0140292048 sf0140291005 1 40292048 4.94E-06 4.94E-06