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 mr1632 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
vg0211188937 sf0211188934 2 11188937 7.99E-13 1.59E-07
vg0216222379 sf0216216509 2 16222379 3.28E-12 1.07E-06
vg0500689055 sf0500689055 5 689055 8.16E-11 NA
vg0216449439 sf0216443569 2 16449439 8.39E-11 1.88E-06
vg1204697263 sf1204696251 12 4697263 9.94E-11 NA
vg1115141729 sf1114678043 11 15141729 2.58E-10 NA
vg0805944662 sf0805943665 8 5944662 4.57E-10 3.37E-06
vg0812621693 sf0812619518 8 12621693 3.49E-09 3.99E-06
vg0207729665 sf0207729664 2 7729665 9.30E-09 NA
vg0713133131 sf0713132138 7 13133131 9.69E-08 1.95E-06
vg0506870350 sf0506870292 5 6870350 2.83E-07 5.87E-08
vg1205848936 sf1205847918 12 5848936 6.68E-07 1.92E-06
vg0817018173 sf0817015459 8 17018173 NA 1.50E-06