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 mr1754 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
vg1216527792 sf1216525085 12 16527792 5.19E-08 5.19E-08
vg1100903458 sf1100902459 11 903458 6.72E-08 6.72E-08
vg0321576069 sf0321574579 3 21576069 5.32E-07 5.32E-07
vg0219279605 sf0219273737 2 19279605 1.14E-06 1.14E-06
vg0714886064 sf0714885071 7 14886064 1.99E-06 1.99E-06
vg0725365802 sf0725364808 7 25365802 2.36E-06 2.36E-06
vg0723310247 sf0723309254 7 23310247 3.26E-06 3.26E-06
vg0905873470 sf0905872470 9 5873470 3.36E-06 3.36E-06
vg0718397736 sf0718396743 7 18397736 3.63E-06 3.63E-06
vg0234823331 sf0234817462 2 34823331 3.73E-06 3.73E-06
vg0718464632 sf0718463639 7 18464632 9.68E-06 9.68E-06