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 mr1911 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
vg0222743508 sf0222737639 2 22743508 1.85E-38 5.08E-30
vg0222724011 sf0222718142 2 22724011 6.37E-38 5.07E-30
vg0222634177 sf0222628308 2 22634177 1.25E-11 5.96E-07
vg0222765370 sf0222759501 2 22765370 2.14E-11 9.45E-07
vg0223637840 sf0223631971 2 23637840 2.05E-09 1.23E-08
vg0222672641 sf0222666772 2 22672641 4.58E-09 9.34E-07
vg0222022581 sf0222016712 2 22022581 6.88E-09 NA
vg0222681985 sf0222676116 2 22681985 4.36E-08 1.81E-10
vg0719444997 sf0719444004 7 19444997 7.34E-08 7.64E-07
vg0222879623 sf0222873754 2 22879623 2.51E-07 1.07E-08
vg0223695952 sf0223690083 2 23695952 3.76E-07 3.51E-08
vg1112606104 sf1112142307 11 12606104 5.33E-07 2.35E-06
vg0719632131 sf0719631138 7 19632131 6.72E-07 NA
vg0222735022 sf0222729153 2 22735022 3.86E-06 4.66E-06
vg0816208909 sf0816206195 8 16208909 NA 4.49E-06
vg0109549917 sf0109548893 1 9549917 NA 4.94E-06
vg1119286482 sf1118820170 11 19286482 NA 8.03E-06