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 mr1403 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
vg0410939481 sf0410930182 4 10939481 5.36E-19 NA
vg0407150917 sf0407146187 4 7150917 9.13E-19 NA
vg0410872426 sf0410863127 4 10872426 1.05E-18 2.66E-06
vg0308386621 sf0308385559 3 8386621 7.21E-15 NA
vg0307717783 sf0307716721 3 7717783 3.81E-14 2.83E-06
vg0432466421 sf0432281313 4 32466421 2.91E-13 NA
vg0820439713 sf0820437000 8 20439713 3.44E-13 NA
vg0432452537 sf0432267429 4 32452537 1.13E-12 1.12E-06
vg0432402949 sf0432217840 4 32402949 3.04E-12 8.78E-08
vg1202876468 sf1202875470 12 2876468 8.97E-09 NA
vg0413090350 sf0413081060 4 13090350 3.18E-08 NA
vg0307639490 sf0307638428 3 7639490 NA 1.65E-07
vg0103148298 sf0103147298 1 3148298 NA 9.02E-07
vg0408360452 sf0408355726 4 8360452 NA 1.02E-06
vg1218165901 sf1218137337 12 18165901 NA 1.54E-06
vg0409509076 sf0409499774 4 9509076 NA 2.91E-06