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 mr1884 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
vg0918912379 sf0918911379 9 18912379 1.69E-07 1.69E-07
vg1104978881 sf1104974692 11 4978881 4.67E-07 4.67E-07
vg1105269119 sf1105264870 11 5269119 1.09E-06 1.09E-06
vg0213822498 sf0213816628 2 13822498 2.43E-06 2.43E-06
vg0718838390 sf0718837397 7 18838390 2.53E-06 2.53E-06
vg0908524458 sf0908523458 9 8524458 2.64E-06 2.64E-06
vg0914989973 sf0914988972 9 14989973 3.67E-06 3.67E-06
vg0526462498 sf0526399861 5 26462498 4.61E-06 4.61E-06