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 mr1967 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
vg0103604713 sf0103603713 1 3604713 4.14E-09 4.14E-09
vg0103185888 sf0103184888 1 3185888 5.90E-08 5.90E-08
vg0102531005 sf0102530005 1 2531005 1.49E-07 1.49E-07
vg1221706812 sf1221673359 12 21706812 4.83E-07 4.83E-07
vg0428087648 sf0427902514 4 28087648 1.92E-06 1.92E-06
vg1224363975 sf1224330428 12 24363975 2.24E-06 2.24E-06
vg0201101756 sf0201101756 2 1101756 2.78E-06 2.78E-06