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 mr1089 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
vg0216752678 sf0216746808 2 16752678 9.01E-35 1.49E-23
vg0217047369 sf0217041499 2 17047369 4.15E-34 7.20E-25
vg0216511882 sf0216506012 2 16511882 4.32E-17 1.76E-09
vg1210626805 sf1210624218 12 10626805 8.93E-16 5.27E-08
vg0213525745 sf0213525741 2 13525745 3.19E-15 7.10E-08
vg0216163383 sf0216157513 2 16163383 5.33E-15 3.47E-06
vg1217578105 sf1217572060 12 17578105 1.21E-14 NA
vg0217737908 sf0217732038 2 17737908 1.28E-13 1.78E-07
vg0216666509 sf0216660639 2 16666509 3.72E-13 1.38E-06
vg0217788689 sf0217782820 2 17788689 3.42E-12 1.06E-06
vg0900336799 sf0900335799 9 336799 6.50E-12 6.13E-07
vg1217366858 sf1217360813 12 17366858 1.14E-11 4.10E-06
vg0218852605 sf0218846736 2 18852605 3.83E-11 1.97E-06
vg0216594685 sf0216588815 2 16594685 1.68E-08 2.19E-09
vg0411806765 sf0411797476 4 11806765 4.01E-08 6.45E-08
vg0315179060 sf0315177707 3 15179060 1.94E-07 3.10E-06
vg0216876069 sf0216870199 2 16876069 2.17E-07 1.54E-07
vg0315572376 sf0315571023 3 15572376 NA 1.99E-06
vg0525534836 sf0525472257 5 25534836 NA 2.43E-06
vg0141497668 sf0141496625 1 41497668 NA 4.62E-06
vg0216616335 sf0216610465 2 16616335 NA 4.66E-06
vg1005364262 sf1005380799 10 5364262 NA 4.91E-06