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 mr1343 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
vg0724529234 sf0724528240 7 24529234 1.84E-22 2.64E-20
vg0331266260 sf0331259145 3 31266260 3.10E-14 2.73E-09
vg0331248975 sf0331241860 3 31248975 8.91E-14 7.94E-10
vg0131772083 sf0131771039 1 31772083 5.17E-12 NA
vg0131775262 sf0131774218 1 31775262 6.83E-12 NA
vg0104005677 sf0104004677 1 4005677 2.33E-10 NA
vg1000401399 sf1000400399 10 401399 3.40E-10 4.84E-07
vg0331236124 sf0331229009 3 31236124 4.48E-10 2.41E-07
vg1117595503 sf1117129360 11 17595503 6.60E-10 5.50E-08
vg0400999452 sf0400995004 4 999452 1.08E-09 3.78E-07
vg0411899064 sf0411889775 4 11899064 3.60E-09 1.20E-07
vg0803154417 sf0803153420 8 3154417 6.57E-08 8.18E-07
vg0325213731 sf0325211812 3 25213731 6.67E-08 1.01E-06
vg0725312603 sf0725311609 7 25312603 1.75E-07 2.43E-06
vg0815721034 sf0815718320 8 15721034 2.54E-07 9.38E-07
vg0724515347 sf0724514353 7 24515347 NA 4.21E-15
vg0724381738 sf0724380744 7 24381738 NA 2.20E-08
vg0724481626 sf0724480632 7 24481626 NA 2.84E-08
vg0411926825 sf0411917536 4 11926825 NA 4.01E-07
vg0724401667 sf0724400673 7 24401667 NA 7.84E-07
vg1117593072 sf1117126929 11 17593072 NA 1.78E-06
vg1201219940 sf1201218940 12 1219940 NA 4.31E-06
vg0312035597 sf0312034315 3 12035597 NA 4.90E-06