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 mr1093 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
vg0216699507 sf0216693637 2 16699507 1.83E-73 3.03E-19
vg0216623044 sf0216617174 2 16623044 1.65E-71 6.22E-20
vg0216803823 sf0216797953 2 16803823 1.21E-51 2.23E-19
vg0216822884 sf0216817014 2 16822884 1.35E-51 2.03E-19
vg1018767336 sf1018695893 10 18767336 9.51E-50 NA
vg0720349785 sf0720348792 7 20349785 1.18E-47 NA
vg0310117701 sf0310116637 3 10117701 1.81E-47 NA
vg1220041122 sf1220012564 12 20041122 2.83E-46 1.16E-06
vg0812023942 sf0812022947 8 12023942 NA 1.43E-10
vg0217233417 sf0217227547 2 17233417 NA 6.67E-08
vg1004584495 sf1004601033 10 4584495 NA 8.08E-07
vg0212179937 sf0212179933 2 12179937 NA 1.08E-06
vg1105770829 sf1105766581 11 5770829 NA 1.27E-06
vg1016575340 sf1016504113 10 16575340 NA 1.90E-06
vg1004582886 sf1004599424 10 4582886 NA 2.08E-06
vg0218664196 sf0218658327 2 18664196 NA 3.03E-06
vg0300876894 sf0300875892 3 876894 NA 3.44E-06
vg0909056772 sf0909055771 9 9056772 NA 5.00E-06