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 mr1082 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
vg0719104847 sf0719103854 7 19104847 1.71E-48 3.14E-29
vg0719049906 sf0719048913 7 19049906 4.66E-48 6.78E-31
vg0708204553 sf0708203558 7 8204553 4.26E-45 1.37E-06
vg0220550093 sf0220544225 2 20550093 6.12E-45 1.19E-06
vg0216352296 sf0216346426 2 16352296 1.56E-43 NA
vg0305690892 sf0305689892 3 5690892 2.15E-43 NA
vg0719156146 sf0719155153 7 19156146 NA 7.53E-21
vg0719091461 sf0719090468 7 19091461 NA 1.38E-17
vg0719067465 sf0719066472 7 19067465 NA 1.33E-14
vg0719345307 sf0719344314 7 19345307 NA 9.04E-14
vg0719140498 sf0719139505 7 19140498 NA 9.48E-13
vg0130826614 sf0130825570 1 30826614 NA 4.35E-12
vg0130813657 sf0130812613 1 30813657 NA 2.31E-11
vg0719373290 sf0719372297 7 19373290 NA 9.60E-11
vg0707699197 sf0707698202 7 7699197 NA 1.06E-10
vg0130825775 sf0130824731 1 30825775 NA 2.65E-09
vg0130667376 sf0130666332 1 30667376 NA 2.93E-09
vg0719466615 sf0719465622 7 19466615 NA 4.26E-09
vg0719436399 sf0719435406 7 19436399 NA 5.49E-09
vg0136510873 sf0136509830 1 36510873 NA 6.85E-09
vg0720529894 sf0720528901 7 20529894 NA 1.24E-08
vg0109818394 sf0109817370 1 9818394 NA 2.14E-08
vg0909775480 sf0909774479 9 9775480 NA 3.18E-08
vg0325008757 sf0325006837 3 25008757 NA 4.85E-08
vg0428494128 sf0428308982 4 28494128 NA 6.45E-08
vg0708794274 sf0708793279 7 8794274 NA 6.78E-08
vg0418083292 sf0417911333 4 18083292 NA 8.35E-08
vg0613280290 sf0613279291 6 13280290 NA 9.36E-08
vg0329561125 sf0329554165 3 29561125 NA 9.89E-08
vg0509310393 sf0509310322 5 9310393 NA 9.92E-08