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 mr1371 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
vg0704732672 sf0704731673 7 4732672 7.35E-08 1.52E-07
vg0709448532 sf0709447538 7 9448532 1.52E-07 2.93E-07
vg0419848656 sf0419676692 4 19848656 3.06E-07 1.13E-06
vg0921004343 sf0921003862 9 21004343 5.76E-07 2.43E-06
vg0607692659 sf0607691660 6 7692659 7.94E-07 5.22E-06
vg0629854146 sf0629853148 6 29854146 9.42E-07 7.65E-07
vg0712843936 sf0712842943 7 12843936 5.42E-06 4.96E-06
vg1116054140 sf1115589012 11 16054140 6.80E-06 1.90E-06