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 mr1555 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
vg0515870259 sf0515812800 5 15870259 2.19E-10 6.70E-06
vg1126045964 sf1125574378 11 26045964 2.22E-09 NA
vg0515869102 sf0515811643 5 15869102 3.00E-09 NA
vg0507091279 sf0507091221 5 7091279 8.06E-09 NA
vg0116143146 sf0116142120 1 16143146 1.07E-08 8.35E-06
vg0720650627 sf0720649634 7 20650627 1.07E-08 NA
vg1003956758 sf1003955734 10 3956758 2.41E-08 NA
vg1209717516 sf1209714925 12 9717516 1.08E-07 1.06E-06
vg1128858545 sf1128335324 11 28858545 4.50E-07 3.42E-06
vg1127979682 sf1127508068 11 27979682 6.28E-06 NA