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 mr1693 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
vg0402373617 sf0402369212 4 2373617 1.02E-09 5.87E-06
vg1011400166 sf1011328985 10 11400166 1.82E-09 8.13E-06
vg1124210586 sf1123744456 11 24210586 7.16E-09 NA
vg0723551233 sf0723550240 7 23551233 1.00E-08 NA
vg0721638290 sf0721637297 7 21638290 1.80E-08 7.83E-06
vg0304878960 sf0304877962 3 4878960 6.87E-08 NA
vg0712529793 sf0712528800 7 12529793 6.90E-08 3.33E-06
vg1120085198 sf1119619121 11 20085198 4.88E-07 2.70E-06
vg0316109457 sf0316108104 3 16109457 1.99E-06 NA
vg1124181870 sf1123715740 11 24181870 6.61E-06 NA