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 mr1547 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
vg1003411947 sf1003410924 10 3411947 7.13E-32 5.22E-23
vg1003402306 sf1003401283 10 3402306 7.32E-32 8.88E-24
vg1003149497 sf1003148474 10 3149497 5.37E-15 7.98E-12
vg0717727326 sf0717726333 7 17727326 5.26E-13 2.36E-08
vg1002838375 sf1002837352 10 2838375 2.10E-12 4.00E-06
vg1003059277 sf1003058254 10 3059277 3.93E-12 4.34E-10
vg0710493875 sf0710492881 7 10493875 2.41E-11 1.15E-06
vg1215306171 sf1215303469 12 15306171 7.86E-11 8.20E-07
vg0717601432 sf0717600439 7 17601432 7.66E-10 1.15E-07
vg0616071895 sf0616070897 6 16071895 1.54E-09 1.86E-08
vg0422509805 sf0422324692 4 22509805 1.70E-09 1.41E-07
vg0623387410 sf0623386413 6 23387410 6.09E-09 4.13E-06
vg0211140215 sf0211140212 2 11140215 4.93E-08 1.09E-06
vg0811933847 sf0811932852 8 11933847 1.03E-07 1.66E-06
vg0618250316 sf0618249319 6 18250316 1.41E-07 1.20E-06