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 mr1770 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
vg1119340990 sf1118874678 11 19340990 7.38E-10 7.38E-10
vg0220076232 sf0220070364 2 20076232 1.18E-07 1.18E-07
vg0219292377 sf0219286509 2 19292377 4.05E-07 4.06E-07
vg0521045026 sf0520982467 5 21045026 5.05E-07 5.05E-07
vg0107845967 sf0107844967 1 7845967 5.41E-07 5.41E-07
vg0141570346 sf0141569303 1 41570346 5.75E-07 5.75E-07
vg0602313316 sf0602312317 6 2313316 9.35E-07 9.35E-07
vg1108064762 sf1108060507 11 8064762 1.10E-06 1.10E-06
vg1105334970 sf1105330721 11 5334970 1.62E-06 1.62E-06
vg0306499925 sf0306498925 3 6499925 1.84E-06 1.84E-06
vg0602342015 sf0602341016 6 2342015 1.90E-06 1.90E-06
vg0221401906 sf0221396038 2 21401906 2.03E-06 2.03E-06
vg0817475785 sf0817473071 8 17475785 2.09E-06 2.10E-06
vg1100495758 sf1100494761 11 495758 2.35E-06 2.35E-06
vg0520889189 sf0520826630 5 20889189 2.98E-06 2.98E-06