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 mr1940 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
vg1002090270 sf1002089247 10 2090270 6.50E-16 NA
vg0819332152 sf0819329439 8 19332152 1.19E-15 NA
vg0919017207 sf0919016207 9 19017207 3.33E-15 NA
vg0912499541 sf0912498540 9 12499541 4.47E-15 NA
vg1203617375 sf1203616374 12 3617375 8.71E-15 NA
vg0426102441 sf0425917316 4 26102441 1.98E-13 3.61E-06
vg1003178529 sf1003177506 10 3178529 2.50E-13 NA
vg0613828471 sf0613827472 6 13828471 1.74E-12 NA
vg0523519263 sf0523456684 5 23519263 NA 9.10E-07
vg0729640266 sf0729639274 7 29640266 NA 4.39E-06
vg1005627516 sf1005644054 10 5627516 NA 9.68E-06