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 mr1973 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
vg0807746311 sf0807745315 8 7746311 2.15E-08 2.15E-08
vg1206162924 sf1206161815 12 6162924 6.92E-08 6.92E-08
vg0420539514 sf0420367558 4 20539514 7.80E-08 7.80E-08
vg0234270181 sf0234264312 2 34270181 1.06E-07 1.06E-07
vg0506760814 sf0506760756 5 6760814 1.07E-07 1.07E-07
vg1202007001 sf1202005999 12 2007001 1.16E-07 1.16E-07
vg1106677250 sf1106673003 11 6677250 2.22E-07 2.22E-07
vg0909578119 sf0909577118 9 9578119 2.51E-07 2.51E-07
vg0713890951 sf0713889958 7 13890951 8.80E-07 8.80E-07
vg0911115830 sf0911114829 9 11115830 9.82E-07 9.82E-07
vg0627259502 sf0627258505 6 27259502 1.22E-06 1.22E-06
vg1100185205 sf1100184206 11 185205 1.34E-06 1.34E-06
vg1202111176 sf1202110174 12 2111176 1.34E-06 1.34E-06
vg0107724143 sf0107723143 1 7724143 1.67E-06 1.67E-06
vg0500074042 sf0500074042 5 74042 1.79E-06 1.79E-06
vg1212036957 sf1212034292 12 12036957 2.36E-06 2.36E-06
vg0809238968 sf0809237972 8 9238968 2.65E-06 2.65E-06
vg1014788162 sf1014716928 10 14788162 2.81E-06 2.81E-06
vg0424198526 sf0424013387 4 24198526 2.95E-06 2.95E-06
vg0822651774 sf0822649061 8 22651774 3.51E-06 3.51E-06