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 mr1779 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
vg0819985140 sf0819982427 8 19985140 1.28E-09 8.29E-06
vg1105604028 sf1105599780 11 5604028 5.20E-09 NA
vg0724945438 sf0724944444 7 24945438 6.10E-09 9.66E-06
vg0133075708 sf0133074664 1 33075708 8.83E-09 NA
vg1103050384 sf1103046288 11 3050384 1.09E-08 NA
vg0819401978 sf0819399265 8 19401978 1.16E-06 NA
vg0724939532 sf0724938538 7 24939532 1.17E-06 NA