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 mr1224 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
vg0719055987 sf0719054994 7 19055987 2.20E-22 2.12E-19
vg0820065663 sf0820062950 8 20065663 1.01E-10 5.01E-09
vg0413556513 sf0413547227 4 13556513 3.58E-09 2.55E-07
vg0108800483 sf0108799483 1 8800483 7.84E-09 1.36E-07
vg1011340029 sf1011268849 10 11340029 9.72E-09 4.57E-06
vg0722044007 sf0722043014 7 22044007 1.05E-08 3.76E-06
vg0230093704 sf0230087835 2 30093704 1.11E-07 1.85E-06
vg1127413102 sf1126941489 11 27413102 2.23E-07 3.00E-06
vg0700322812 sf0700321812 7 322812 3.65E-07 2.81E-06