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 mr1539 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
vg1216413002 sf1216410295 12 16413002 1.65E-22 NA
vg1018873646 sf1018802202 10 18873646 3.91E-22 NA
vg1125230825 sf1124764665 11 25230825 4.27E-22 NA
vg0520385810 sf0520323282 5 20385810 7.48E-22 NA
vg0129829417 sf0129828372 1 29829417 1.08E-21 NA
vg0132537682 sf0132536638 1 32537682 1.79E-21 7.99E-07
vg0122899113 sf0122898069 1 22899113 2.49E-21 4.46E-06
vg0520294036 sf0520231509 5 20294036 2.76E-20 NA
vg0129921541 sf0129920496 1 29921541 3.52E-20 3.12E-07
vg1122054525 sf1121588396 11 22054525 2.03E-19 1.52E-06
vg1208083877 sf1208081283 12 8083877 6.17E-18 4.83E-07
vg0129848686 sf0129847641 1 29848686 NA 1.16E-08
vg0805342735 sf0805341738 8 5342735 NA 1.35E-06
vg0121972302 sf0121971257 1 21972302 NA 1.59E-06
vg1120477715 sf1120011640 11 20477715 NA 2.42E-06
vg0726783003 sf0726782009 7 26783003 NA 2.67E-06
vg0132542635 sf0132541591 1 32542635 NA 3.89E-06
vg1120481051 sf1120014976 11 20481051 NA 5.36E-06