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 mr1803 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
vg1215976655 sf1215973951 12 15976655 4.60E-13 1.09E-07
vg1210519897 sf1210517310 12 10519897 2.03E-12 2.59E-08
vg1217578105 sf1217572060 12 17578105 2.51E-12 2.06E-08
vg1215615147 sf1215612444 12 15615147 3.50E-11 2.81E-08
vg1210023864 sf1210021275 12 10023864 4.36E-10 8.17E-09
vg1211970311 sf1211967646 12 11970311 1.15E-09 1.76E-06
vg0114066007 sf0114064981 1 14066007 2.76E-09 NA
vg0912288601 sf0912287600 9 12288601 3.33E-06 1.71E-06
vg1123726533 sf1123260403 11 23726533 NA 1.15E-06
vg0121510990 sf0121509945 1 21510990 NA 1.61E-06