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 mr1379 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
vg0907974545 sf0907973545 9 7974545 1.10E-08 NA
vg1004020304 sf1004019280 10 4020304 1.19E-08 NA
vg1005318536 sf1005335073 10 5318536 1.34E-08 4.76E-06
vg0202831799 sf0202831797 2 2831799 1.37E-08 NA
vg1006382367 sf1006397990 10 6382367 1.50E-08 NA
vg0325696417 sf0325694435 3 25696417 2.14E-08 1.19E-10
vg0400345487 sf0400344487 4 345487 4.76E-07 1.41E-07
vg0216756385 sf0216750515 2 16756385 5.65E-06 NA
vg0612772228 sf0612771229 6 12772228 6.19E-06 NA
vg1212822297 sf1212819636 12 12822297 8.18E-06 NA
vg0415028838 sf0415019552 4 15028838 NA 3.55E-06