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 mr1257 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
vg0216800422 sf0216794552 2 16800422 1.06E-97 4.05E-35
vg0216673252 sf0216667382 2 16673252 2.95E-49 3.35E-09
vg0213525745 sf0213525741 2 13525745 9.81E-48 1.68E-11
vg0216763637 sf0216757767 2 16763637 1.20E-46 7.56E-13
vg0216740793 sf0216734923 2 16740793 2.32E-46 1.06E-13
vg0900337327 sf0900336327 9 337327 1.75E-42 2.97E-10
vg0719969082 sf0719968089 7 19969082 4.63E-42 NA
vg0812023942 sf0812022947 8 12023942 1.48E-37 1.62E-06
vg1114473442 sf1114009759 11 14473442 2.28E-37 2.94E-06
vg0228028944 sf0228023075 2 28028944 1.74E-34 3.99E-06
vg1220237342 sf1220208784 12 20237342 7.06E-34 1.55E-06
vg0217254952 sf0217249082 2 17254952 NA 3.93E-18
vg0217327456 sf0217321586 2 17327456 NA 5.21E-09
vg0216380390 sf0216374520 2 16380390 NA 6.14E-08
vg0217812245 sf0217806376 2 17812245 NA 8.14E-08
vg0216821215 sf0216815345 2 16821215 NA 5.43E-07
vg0217025794 sf0217019924 2 17025794 NA 6.16E-07
vg1005364262 sf1005380799 10 5364262 NA 1.90E-06
vg0719447778 sf0719446785 7 19447778 NA 2.75E-06
vg0133242822 sf0133241778 1 33242822 NA 3.53E-06
vg0210766159 sf0210766157 2 10766159 NA 3.90E-06