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 mr1627 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
vg0308491408 sf0308490346 3 8491408 1.10E-28 NA
vg0910847099 sf0910846098 9 10847099 1.37E-28 3.26E-06
vg0523046901 sf0522984342 5 23046901 2.31E-26 NA
vg0828050045 sf0828047331 8 28050045 2.66E-26 NA
vg0910745951 sf0910744950 9 10745951 6.32E-26 1.21E-06
vg0141896454 sf0141895411 1 41896454 6.67E-26 NA
vg0819989626 sf0819986913 8 19989626 5.10E-25 1.79E-06
vg0103397447 sf0103396447 1 3397447 9.94E-23 1.24E-06
vg0200390756 sf0200390756 2 390756 9.80E-21 NA
vg1214853500 sf1214850841 12 14853500 3.12E-20 5.10E-06
vg0312533516 sf0312532234 3 12533516 1.50E-19 NA
vg0910734707 sf0910733706 9 10734707 NA 1.11E-09
vg0414404728 sf0414395441 4 14404728 NA 3.95E-08
vg0117252176 sf0117251130 1 17252176 NA 5.70E-08
vg0512704119 sf0512647041 5 12704119 NA 8.88E-08
vg0122037982 sf0122036937 1 22037982 NA 1.56E-07
vg0711963821 sf0711962827 7 11963821 NA 1.09E-06
vg0721381168 sf0721380175 7 21381168 NA 4.05E-06
vg0910743892 sf0910742891 9 10743892 NA 4.40E-06