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 mr1243 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
vg0216763637 sf0216757767 2 16763637 1.07E-13 7.12E-09
vg0901298066 sf0901297066 9 1298066 7.21E-11 7.15E-08
vg0506159272 sf0506159211 5 6159272 5.59E-10 NA
vg0220627301 sf0220621433 2 20627301 1.63E-09 NA
vg0222533839 sf0222527970 2 22533839 3.21E-09 NA
vg0432630329 sf0432445218 4 32630329 3.78E-09 7.63E-07
vg0803628301 sf0803627304 8 3628301 4.12E-09 1.86E-06
vg0614036364 sf0614035365 6 14036364 5.07E-09 2.62E-06
vg0505521761 sf0505521699 5 5521761 1.43E-08 2.43E-06
vg0620421716 sf0620420719 6 20421716 1.81E-07 3.08E-06