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 mr1341 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
vg0622361473 sf0622360476 6 22361473 3.87E-10 2.90E-06
vg0611453377 sf0611452378 6 11453377 1.19E-09 NA
vg1202061889 sf1202060887 12 2061889 4.70E-09 2.53E-06
vg1000566988 sf1000565964 10 566988 8.15E-09 4.59E-07
vg0219673660 sf0219667792 2 19673660 2.24E-08 5.01E-06
vg0627850120 sf0627849122 6 27850120 3.22E-08 1.88E-06
vg1109865508 sf1109860085 11 9865508 9.84E-07 3.77E-06
vg0900240306 sf0900239306 9 240306 1.77E-06 4.88E-07
vg0809087399 sf0809086403 8 9087399 1.89E-06 8.65E-07
vg0300892445 sf0300891443 3 892445 NA 3.54E-06