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 mr1074 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
vg0130670983 sf0130669939 1 30670983 3.49E-15 3.49E-15
vg0130845945 sf0130844901 1 30845945 2.57E-08 2.57E-08
vg0722488401 sf0722487408 7 22488401 8.18E-07 8.18E-07
vg0138784720 sf0138783677 1 38784720 1.12E-06 1.12E-06
vg0800134286 sf0800133286 8 134286 1.23E-06 1.23E-06
vg1200440277 sf1200439277 12 440277 1.28E-06 1.28E-06
vg0622306774 sf0622305777 6 22306774 1.66E-06 1.66E-06
vg1227115867 sf1227082266 12 27115867 1.89E-06 1.89E-06
vg0136199234 sf0136198191 1 36199234 2.23E-06 2.23E-06
vg0102113172 sf0102112172 1 2113172 3.07E-06 3.07E-06
vg0505168151 sf0505168129 5 5168151 3.25E-06 3.25E-06
vg1213663935 sf1213661273 12 13663935 3.46E-06 3.46E-06
vg0130038156 sf0130037111 1 30038156 3.76E-06 3.76E-06
vg0142433667 sf0142432623 1 42433667 3.92E-06 3.92E-06
vg0709186195 sf0709185201 7 9186195 4.70E-06 4.70E-06
vg0900735028 sf0900734028 9 735028 4.70E-06 4.70E-06