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 mr1943 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
vg0106328375 sf0106327375 1 6328375 4.65E-27 7.39E-06
vg0118901136 sf0118900091 1 18901136 1.83E-26 1.77E-06
vg0333264147 sf0333257017 3 33264147 1.84E-25 NA
vg0503683293 sf0503683270 5 3683293 2.59E-25 NA
vg1125153977 sf1124687817 11 25153977 2.60E-25 NA
vg0303683317 sf0303682313 3 3683317 7.23E-25 NA
vg1218167970 sf1218139406 12 18167970 8.60E-24 4.74E-06
vg0813601775 sf0813599060 8 13601775 NA 6.50E-08
vg1215172595 sf1215169931 12 15172595 NA 4.09E-07
vg1215653812 sf1215651109 12 15653812 NA 9.62E-07
vg1125073787 sf1124607627 11 25073787 NA 2.00E-06
vg1215352870 sf1215350168 12 15352870 NA 2.89E-06
vg0320923321 sf0320921831 3 20923321 NA 3.02E-06