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 mr1314 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 1.94E-08 NA
vg0301361367 sf0301360365 3 1361367 4.77E-07 NA
vg1218165628 sf1218137064 12 18165628 9.88E-06 1.43E-06
vg0103143509 sf0103142509 1 3143509 NA 2.06E-07
vg1215653812 sf1215651109 12 15653812 NA 1.79E-06
vg0406853946 sf0406849391 4 6853946 NA 1.80E-06
vg1214068891 sf1214066231 12 14068891 NA 2.20E-06
vg1217052179 sf1217046133 12 17052179 NA 4.19E-06
vg0318942572 sf0318941332 3 18942572 NA 4.26E-06
vg1217057480 sf1217051435 12 17057480 NA 4.70E-06
vg0406854032 sf0406849477 4 6854032 NA 5.66E-06