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 mr1602 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
vg0305333401 sf0305332401 3 5333401 5.25E-10 6.19E-08
vg0400003186 sf0400002186 4 3186 6.41E-10 2.05E-06
vg0335763672 sf0335756541 3 35763672 1.78E-09 1.18E-06
vg0716931835 sf0716930842 7 16931835 2.60E-09 3.77E-06
vg0418087592 sf0417915633 4 18087592 2.75E-09 2.78E-06
vg0420667247 sf0420495290 4 20667247 1.04E-08 1.43E-06
vg0405134587 sf0405130029 4 5134587 3.19E-07 1.85E-07
vg1213955091 sf1213952431 12 13955091 3.88E-07 7.18E-06
vg0405116756 sf0405112198 4 5116756 1.03E-06 6.08E-08
vg1218237165 sf1218208601 12 18237165 NA 9.13E-07
vg0712030137 sf0712029143 7 12030137 NA 1.79E-06
vg1001307681 sf1001306658 10 1307681 NA 2.66E-06
vg1214271899 sf1214269239 12 14271899 NA 3.09E-06
vg1218165628 sf1218137064 12 18165628 NA 3.18E-06
vg0307880743 sf0307879681 3 7880743 NA 4.93E-06