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 mr1032 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
vg0610871475 sf0610870476 6 10871475 4.60E-20 1.32E-08
vg0524588276 sf0524525696 5 24588276 5.32E-18 NA
vg1100066353 sf1100065353 11 66353 5.46E-18 NA
vg0205541527 sf0205541527 2 5541527 6.67E-18 NA
vg0920193283 sf0920192802 9 20193283 9.15E-17 NA
vg0615627431 sf0615626433 6 15627431 1.08E-14 NA
vg1004623685 sf1004640223 10 4623685 5.08E-14 9.79E-08
vg0502125341 sf0502125315 5 2125341 9.08E-14 6.25E-09
vg0608916603 sf0608915604 6 8916603 NA 4.11E-07
vg1004568048 sf1004584586 10 4568048 NA 6.18E-07
vg0419746635 sf0419574670 4 19746635 NA 1.37E-06
vg1207394291 sf1207391698 12 7394291 NA 4.06E-06
vg1004572201 sf1004588739 10 4572201 NA 4.62E-06
vg1210252343 sf1210249755 12 10252343 NA 5.99E-06
vg0727995401 sf0727994408 7 27995401 NA 8.54E-06