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 mr1406 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
vg0429999261 sf0429814128 4 29999261 2.88E-10 3.36E-06
vg0102177582 sf0102176582 1 2177582 5.24E-09 2.42E-06
vg0803976100 sf0803975103 8 3976100 8.79E-09 NA
vg0429753312 sf0429568181 4 29753312 1.71E-08 1.20E-07
vg0429752463 sf0429567332 4 29752463 1.82E-08 1.28E-07
vg0129430227 sf0129429182 1 29430227 3.11E-08 NA
vg0810160289 sf0810159293 8 10160289 4.20E-08 NA
vg0724397000 sf0724396006 7 24397000 2.65E-07 8.31E-07
vg0724529647 sf0724528653 7 24529647 6.20E-07 5.28E-07
vg0824284842 sf0824282128 8 24284842 8.49E-07 3.72E-06
vg0724504072 sf0724503078 7 24504072 1.46E-06 1.88E-07
vg0429812608 sf0429627479 4 29812608 2.05E-06 3.94E-06
vg0518984986 sf0518922470 5 18984986 NA 1.15E-07
vg0432443707 sf0432258598 4 32443707 NA 2.13E-06
vg0322579188 sf0322577677 3 22579188 NA 2.15E-06
vg0721954637 sf0721953644 7 21954637 NA 2.50E-06
vg0920188922 sf0920188441 9 20188922 NA 3.27E-06
vg0130137856 sf0130136811 1 30137856 NA 4.85E-06
vg0432449081 sf0432263973 4 32449081 NA 8.66E-06