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 mr1570 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
vg0609100240 sf0609099241 6 9100240 6.19E-20 7.89E-11
vg0609099267 sf0609098268 6 9099267 2.28E-19 5.97E-11
vg0207732987 sf0207732986 2 7732987 1.97E-16 1.84E-10
vg1206223802 sf1206222692 12 6223802 1.12E-14 NA
vg0906567849 sf0906566849 9 6567849 1.07E-13 NA
vg1121466812 sf1121000689 11 21466812 1.11E-13 NA
vg0608672147 sf0608671148 6 8672147 1.94E-11 8.65E-09
vg0611149150 sf0611148151 6 11149150 5.32E-09 5.00E-07
vg0609055058 sf0609054059 6 9055058 NA 2.85E-07
vg1119511230 sf1119044918 11 19511230 NA 9.05E-07
vg0324095158 sf0324093237 3 24095158 NA 1.98E-06
vg0910714998 sf0910713997 9 10714998 NA 2.42E-06
vg0609225907 sf0609224908 6 9225907 NA 2.57E-06
vg0608187758 sf0608186759 6 8187758 NA 2.89E-06
vg0907502049 sf0907501049 9 7502049 NA 5.66E-06