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 mr1291 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
vg0336243988 sf0336236914 3 36243988 1.23E-08 2.56E-07
vg1100083618 sf1100082618 11 83618 1.31E-08 NA
vg1208804843 sf1208802250 12 8804843 1.63E-08 5.80E-06
vg0133051841 sf0133050797 1 33051841 5.30E-08 NA
vg1222403923 sf1222370362 12 22403923 6.55E-08 NA
vg0617895267 sf0617894270 6 17895267 1.57E-07 9.06E-06
vg0727614620 sf0727613626 7 27614620 1.71E-07 NA
vg0428107534 sf0427922399 4 28107534 1.89E-07 NA
vg0200794640 sf0200794640 2 794640 7.33E-06 NA
vg1009640159 sf1009568980 10 9640159 NA 2.65E-06