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 mr1388 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
vg0818218008 sf0818215295 8 18218008 2.49E-12 NA
vg0820892944 sf0820890231 8 20892944 2.95E-12 NA
vg0329857775 sf0329850814 3 29857775 3.18E-12 9.82E-07
vg0420667247 sf0420495290 4 20667247 4.23E-12 7.23E-06
vg0333751626 sf0333744496 3 33751626 6.21E-12 NA
vg1214365378 sf1214362718 12 14365378 1.02E-11 5.44E-07
vg1214375050 sf1214372391 12 14375050 1.73E-11 9.81E-07
vg0221431941 sf0221426073 2 21431941 6.76E-09 2.42E-07
vg0719058656 sf0719057663 7 19058656 NA 4.06E-07
vg0628127868 sf0628126870 6 28127868 NA 1.14E-06
vg0211199232 sf0211199229 2 11199232 NA 2.25E-06