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 mr1328 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
vg1017130116 sf1017058888 10 17130116 3.08E-08 NA
vg1003175110 sf1003174087 10 3175110 4.81E-08 NA
vg1125360972 sf1124894812 11 25360972 5.37E-08 NA
vg0308383505 sf0308382443 3 8383505 1.68E-07 3.91E-06
vg1017178526 sf1017107299 10 17178526 6.23E-07 NA
vg0103324572 sf0103323572 1 3324572 3.79E-06 8.10E-07
vg0212193592 sf0212193588 2 12193592 NA 7.67E-07
vg0212064522 sf0212064518 2 12064522 NA 9.90E-07
vg0520829830 sf0520767271 5 20829830 NA 3.00E-06