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 mr1777 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
vg0406871855 sf0406867300 4 6871855 1.90E-09 1.90E-09
vg0406987099 sf0406982370 4 6987099 7.30E-07 7.30E-07
vg0131153363 sf0131152319 1 31153363 7.61E-07 7.62E-07
vg1000798980 sf1000797956 10 798980 1.12E-06 1.12E-06
vg0816207758 sf0816205044 8 16207758 1.33E-06 1.33E-06
vg0217652051 sf0217646181 2 17652051 2.02E-06 2.02E-06
vg0412011347 sf0412002058 4 12011347 2.53E-06 2.53E-06
vg0411387439 sf0411378142 4 11387439 3.10E-06 3.10E-06
vg0608613111 sf0608612112 6 8613111 3.34E-06 3.34E-06
vg1104747649 sf1104743551 11 4747649 4.70E-06 4.71E-06