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 mr1530 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
vg1125498126 sf1125031965 11 25498126 1.81E-13 3.42E-07
vg1125388576 sf1124922415 11 25388576 2.87E-13 7.77E-08
vg0619805967 sf0619804970 6 19805967 1.73E-09 NA
vg0616479820 sf0616478822 6 16479820 2.28E-09 NA
vg0611910663 sf0611909664 6 11910663 5.97E-09 NA
vg0432437759 sf0432252650 4 32437759 1.51E-08 NA
vg0114199955 sf0114198929 1 14199955 8.17E-08 6.73E-06
vg1208286382 sf1208283788 12 8286382 3.30E-07 4.13E-06
vg1208286528 sf1208283934 12 8286528 3.40E-07 4.75E-06
vg0809321610 sf0809320614 8 9321610 5.06E-07 4.60E-06
vg0118950790 sf0118949745 1 18950790 1.40E-06 NA
vg0827835751 sf0827833037 8 27835751 NA 1.85E-06
vg0114943457 sf0114942431 1 14943457 NA 4.72E-06