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 mr1362 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
vg0726847020 sf0726846026 7 26847020 4.66E-09 7.79E-07
vg0401302211 sf0401297761 4 1302211 9.29E-09 7.36E-07
vg0817748273 sf0817745560 8 17748273 1.71E-08 2.93E-07
vg0700688176 sf0700687176 7 688176 6.41E-08 NA
vg0908699572 sf0908698571 9 8699572 9.71E-08 NA
vg1116975152 sf1116508993 11 16975152 2.66E-06 NA
vg1106375766 sf1106371518 11 6375766 5.06E-06 4.69E-06
vg0403290283 sf0403285886 4 3290283 NA 2.16E-06