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 mr1820 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
vg1122514350 sf1122048221 11 22514350 1.70E-08 8.01E-06
vg0713417596 sf0713416603 7 13417596 3.04E-07 1.81E-06
vg1214140710 sf1214138050 12 14140710 3.59E-06 4.37E-07
vg1004023838 sf1004022814 10 4023838 8.21E-06 NA
vg1213935504 sf1213932842 12 13935504 9.03E-06 5.27E-07
vg1218126488 sf1218097924 12 18126488 NA 1.21E-06
vg1119465166 sf1118998854 11 19465166 NA 4.09E-06
vg0819258148 sf0819255435 8 19258148 NA 4.40E-06
vg1110517362 sf1110511907 11 10517362 NA 5.62E-06
vg1218168027 sf1218139463 12 18168027 NA 5.75E-06
vg1215653812 sf1215651109 12 15653812 NA 7.74E-06