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 mr1734 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
vg0229433488 sf0229427619 2 29433488 3.51E-16 NA
vg0725111360 sf0725110366 7 25111360 2.86E-15 NA
vg0917754653 sf0917753652 9 17754653 1.65E-14 NA
vg0725262412 sf0725261418 7 25262412 1.84E-14 NA
vg0232699410 sf0232693541 2 32699410 2.31E-14 NA
vg0616361026 sf0616360028 6 16361026 2.64E-14 NA
vg0619697887 sf0619696890 6 19697887 2.02E-13 NA
vg0228836104 sf0228830235 2 28836104 2.19E-12 NA
vg1124866431 sf1124400271 11 24866431 NA 2.05E-06
vg0118775740 sf0118774695 1 18775740 NA 2.19E-06
vg0107647091 sf0107646091 1 7647091 NA 4.58E-06