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 mr1145 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
vg0719051231 sf0719050238 7 19051231 1.52E-37 1.65E-18
vg0719208938 sf0719207945 7 19208938 1.97E-36 3.67E-12
vg0708056089 sf0708055094 7 8056089 1.82E-32 5.18E-06
vg0708222929 sf0708221934 7 8222929 3.20E-32 1.48E-06
vg0612905536 sf0612904537 6 12905536 9.91E-32 NA
vg0704640391 sf0704639392 7 4640391 2.10E-31 NA
vg1017974502 sf1017903274 10 17974502 1.04E-30 NA
vg0215999292 sf0215993422 2 15999292 2.60E-30 4.84E-06
vg0305421774 sf0305420774 3 5421774 8.83E-30 2.24E-06
vg0719191462 sf0719190469 7 19191462 NA 3.52E-12
vg0719055344 sf0719054351 7 19055344 NA 2.30E-09
vg0719345198 sf0719344205 7 19345198 NA 4.45E-09
vg0720529894 sf0720528901 7 20529894 NA 2.32E-08
vg0707699197 sf0707698202 7 7699197 NA 3.94E-07
vg0719449907 sf0719448914 7 19449907 NA 4.23E-07
vg1217486266 sf1217480221 12 17486266 NA 4.81E-07
vg0708155828 sf0708154833 7 8155828 NA 6.25E-07
vg0130825775 sf0130824731 1 30825775 NA 9.02E-07
vg0606529256 sf0606528257 6 6529256 NA 1.60E-06
vg0718956226 sf0718955233 7 18956226 NA 1.64E-06
vg0607478609 sf0607477610 6 7478609 NA 3.65E-06