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 mr1825 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
vg1116207594 sf1115742464 11 16207594 1.59E-08 4.89E-06
vg0304710633 sf0304709635 3 4710633 3.11E-08 2.14E-06
vg1110586892 sf1110581437 11 10586892 4.11E-08 NA
vg1209962192 sf1209959602 12 9962192 7.28E-07 2.22E-06
vg1214629307 sf1214626647 12 14629307 9.77E-07 1.40E-06
vg1102854048 sf1102849952 11 2854048 4.62E-06 3.24E-06
vg0141568520 sf0141567477 1 41568520 5.48E-06 3.40E-06
vg0141568411 sf0141567368 1 41568411 9.14E-06 8.92E-06