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 mr1281 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
vg0525403061 sf0525340482 5 25403061 2.42E-21 NA
vg0314576155 sf0314574842 3 14576155 2.10E-20 6.50E-07
vg0828022358 sf0828019644 8 28022358 2.17E-20 NA
vg0608352038 sf0608351039 6 8352038 3.39E-20 3.65E-06
vg0702503501 sf0702502502 7 2503501 3.45E-20 NA
vg0421026153 sf0420854206 4 21026153 8.15E-20 NA
vg0608355357 sf0608354358 6 8355357 9.36E-20 3.02E-06
vg0724501205 sf0724500211 7 24501205 NA 1.69E-08
vg0618487881 sf0618486884 6 18487881 NA 1.36E-07
vg1217879064 sf1217850498 12 17879064 NA 6.45E-07
vg1005832870 sf1005849408 10 5832870 NA 1.17E-06
vg1123292846 sf1122826716 11 23292846 NA 1.20E-06
vg1012299970 sf1012228785 10 12299970 NA 1.88E-06
vg1012340629 sf1012269444 10 12340629 NA 2.46E-06
vg0725312603 sf0725311609 7 25312603 NA 2.62E-06
vg0710966151 sf0710965157 7 10966151 NA 2.70E-06
vg1013735753 sf1013664522 10 13735753 NA 3.19E-06
vg0234359485 sf0234353616 2 34359485 NA 4.02E-06