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 mr1537 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
vg0715986280 sf0715985287 7 15986280 1.49E-29 NA
vg0400167321 sf0400166321 4 167321 4.90E-29 NA
vg0520100622 sf0520038097 5 20100622 1.30E-28 NA
vg0702509111 sf0702508112 7 2509111 5.31E-28 NA
vg0334602600 sf0334595470 3 34602600 1.25E-27 NA
vg0107301008 sf0107300008 1 7301008 6.98E-26 NA
vg0813522740 sf0813520293 8 13522740 NA 2.10E-06
vg0726456019 sf0726455025 7 26456019 NA 2.99E-06
vg0406835352 sf0406830797 4 6835352 NA 3.08E-06
vg0406883539 sf0406878798 4 6883539 NA 4.57E-06