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 mr1643 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
vg0818230180 sf0818227467 8 18230180 9.28E-08 9.29E-08
vg1013275525 sf1013204295 10 13275525 1.12E-06 1.12E-06
vg0614879232 sf0614878233 6 14879232 1.28E-06 1.28E-06
vg1118715674 sf1118249482 11 18715674 1.55E-06 1.55E-06
vg0818666272 sf0818663559 8 18666272 1.65E-06 1.65E-06
vg0225965623 sf0225959754 2 25965623 1.69E-06 1.69E-06
vg1122514350 sf1122048221 11 22514350 2.89E-06 2.89E-06
vg0623438254 sf0623437257 6 23438254 3.19E-06 3.19E-06
vg0315350100 sf0315348747 3 15350100 3.56E-06 3.56E-06
vg1001246161 sf1001245138 10 1246161 4.69E-06 4.69E-06
vg0200334269 sf0200334269 2 334269 4.95E-06 4.95E-06