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 mr1355 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
vg0100485623 sf0100484623 1 485623 2.18E-09 NA
vg0107647091 sf0107646091 1 7647091 2.80E-09 1.08E-08
vg1103108961 sf1103104864 11 3108961 4.00E-09 9.41E-06
vg0308212263 sf0308211201 3 8212263 5.84E-09 4.59E-06
vg1122521214 sf1122055085 11 22521214 8.28E-09 NA
vg0308157789 sf0308156727 3 8157789 3.77E-08 NA
vg1106023109 sf1106018861 11 6023109 1.05E-07 NA
vg0404020832 sf0404016439 4 4020832 3.57E-07 3.67E-06
vg0616054262 sf0616053264 6 16054262 NA 1.41E-06
vg0614282747 sf0614281748 6 14282747 NA 1.43E-06
vg0613545500 sf0613544501 6 13545500 NA 4.50E-06