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 mr1946 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
vg0224842358 sf0224836489 2 24842358 6.32E-09 2.41E-07
vg1214761316 sf1214758657 12 14761316 7.40E-09 1.14E-07
vg0321582759 sf0321581269 3 21582759 1.13E-08 1.13E-08
vg0232077620 sf0232071751 2 32077620 1.32E-08 5.53E-07
vg0300262673 sf0300261673 3 262673 2.86E-08 3.78E-06
vg0610909238 sf0610908239 6 10909238 1.54E-07 3.67E-06
vg0414329245 sf0414319958 4 14329245 1.80E-07 NA
vg0419845926 sf0419673962 4 19845926 1.89E-07 8.96E-07
vg0415051891 sf0415042606 4 15051891 2.50E-07 4.22E-06
vg0611181245 sf0611180246 6 11181245 3.62E-07 4.83E-06
vg0529058769 sf0528996124 5 29058769 4.34E-07 3.58E-06
vg0504904086 sf0504904064 5 4904086 7.81E-07 4.89E-07
vg0408412077 sf0408407351 4 8412077 1.07E-06 NA
vg0822916694 sf0822913981 8 22916694 1.27E-06 2.53E-06
vg0713683070 sf0713682077 7 13683070 3.45E-06 1.91E-06