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 mr1291 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
vg0101173938 sf0101172938 1 1173938 2.46E-12 NA
vg0329602113 sf0329595153 3 29602113 1.42E-11 NA
vg0322577580 sf0322576069 3 22577580 2.94E-10 NA
vg0140474219 sf0140473176 1 40474219 4.56E-10 NA
vg0107259201 sf0107258201 1 7259201 6.49E-10 NA
vg0122421655 sf0122420610 1 22421655 1.28E-09 3.39E-06
vg0141990004 sf0141988961 1 41990004 1.05E-08 1.76E-06
vg0122451262 sf0122450217 1 22451262 1.16E-08 NA
vg0336113969 sf0336106895 3 36113969 7.20E-08 5.93E-06
vg0617662889 sf0617661892 6 17662889 1.25E-06 NA
vg1105364935 sf1105360686 11 5364935 3.20E-06 NA
vg0420830788 sf0420658831 4 20830788 NA 3.10E-06