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 mr1089 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 6.20E-79 1.88E-16
vg0216763637 sf0216757767 2 16763637 4.90E-76 1.29E-18
vg0216822884 sf0216817014 2 16822884 4.88E-61 5.43E-23
vg0719969082 sf0719968089 7 19969082 1.95E-59 NA
vg0402172640 sf0402168235 4 2172640 3.50E-59 4.31E-07
vg0311456991 sf0311455709 3 11456991 4.71E-59 NA
vg0402172542 sf0402168137 4 2172542 4.45E-58 3.02E-09
vg0217232931 sf0217227061 2 17232931 NA 1.80E-10
vg0130732040 sf0130730996 1 30732040 NA 2.86E-09
vg0130644853 sf0130643809 1 30644853 NA 3.34E-09
vg0213525745 sf0213525741 2 13525745 NA 1.08E-07
vg0900337327 sf0900336327 9 337327 NA 2.77E-07
vg0216636079 sf0216630209 2 16636079 NA 6.34E-07
vg0217270732 sf0217264862 2 17270732 NA 1.09E-06
vg0620204835 sf0620203838 6 20204835 NA 4.18E-06
vg0720878455 sf0720877462 7 20878455 NA 4.46E-06
vg0809520451 sf0809519455 8 9520451 NA 4.84E-06