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 mr1890 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
vg0921847884 sf0921847403 9 21847884 4.32E-55 NA
vg1014788162 sf1014716928 10 14788162 1.52E-54 2.60E-06
vg0304900188 sf0304899190 3 4900188 1.32E-53 NA
vg0332485398 sf0332478271 3 32485398 2.81E-53 NA
vg0827202544 sf0827199830 8 27202544 1.11E-52 NA
vg0528836237 sf0528773592 5 28836237 NA 8.10E-08
vg0805950842 sf0805949845 8 5950842 NA 3.16E-07
vg0400503563 sf0400502561 4 503563 NA 5.31E-07
vg1207830535 sf1207827941 12 7830535 NA 9.23E-07
vg1120477715 sf1120011640 11 20477715 NA 3.99E-06