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 mr1215 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
vg0611950209 sf0611949210 6 11950209 9.75E-15 1.93E-06
vg0725367049 sf0725366055 7 25367049 3.00E-14 NA
vg0610429989 sf0610428990 6 10429989 3.31E-14 9.81E-07
vg0617359224 sf0617358227 6 17359224 7.41E-13 NA
vg0130089111 sf0130088066 1 30089111 1.29E-12 NA
vg0821970212 sf0821967499 8 21970212 6.49E-12 NA
vg1108671225 sf1108665835 11 8671225 3.15E-09 NA
vg1111934896 sf1111929213 11 11934896 3.24E-09 5.94E-06
vg0612016547 sf0612015548 6 12016547 2.88E-08 1.32E-07
vg0720611323 sf0720610330 7 20611323 4.86E-08 NA
vg1215167085 sf1215164421 12 15167085 1.36E-07 1.30E-06
vg1214822308 sf1214819649 12 14822308 NA 5.58E-07
vg0401720392 sf0401715941 4 1720392 NA 3.61E-06