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 mr1908 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
vg0123628790 sf0123627746 1 23628790 1.12E-14 8.87E-06
vg1126542743 sf1126071158 11 26542743 1.29E-13 6.75E-10
vg1125786368 sf1125320289 11 25786368 9.69E-13 4.62E-07
vg0307490488 sf0307489426 3 7490488 2.68E-12 NA
vg0619445566 sf0619444569 6 19445566 5.53E-12 NA
vg0122413949 sf0122412904 1 22413949 2.22E-11 1.03E-06
vg1126497827 sf1126026241 11 26497827 7.81E-10 2.97E-07
vg1121472427 sf1121006304 11 21472427 7.18E-08 NA
vg0516005213 sf0515947721 5 16005213 7.97E-08 NA
vg1127692555 sf1127220942 11 27692555 1.14E-06 2.69E-06
vg0123665592 sf0123664548 1 23665592 1.16E-06 5.21E-07
vg1101201264 sf1101200265 11 1201264 NA 2.60E-07
vg0141059016 sf0141057973 1 41059016 NA 9.88E-07
vg0230921795 sf0230915926 2 30921795 NA 3.67E-06
vg0233057746 sf0233051877 2 33057746 NA 9.73E-06