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 mr1767 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
vg0205287313 sf0205287311 2 5287313 2.07E-28 2.73E-09
vg0205289391 sf0205289389 2 5289391 4.12E-28 2.58E-09
vg1113344086 sf1112880407 11 13344086 3.80E-23 NA
vg0915451165 sf0915450164 9 15451165 7.41E-23 NA
vg1200773837 sf1200772837 12 773837 1.29E-22 NA
vg0129980827 sf0129979782 1 29980827 2.89E-22 NA
vg1119461292 sf1118994980 11 19461292 5.14E-20 NA
vg0402783378 sf0402778983 4 2783378 NA 2.42E-06
vg0414468804 sf0414459517 4 14468804 NA 3.15E-06
vg0222201226 sf0222195357 2 22201226 NA 4.91E-06