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 mr1561 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
vg0123550945 sf0123549901 1 23550945 2.91E-12 NA
vg0122403766 sf0122402721 1 22403766 5.44E-12 1.46E-06
vg0122402401 sf0122401356 1 22402401 5.71E-12 8.11E-07
vg0122407829 sf0122406784 1 22407829 1.14E-10 2.64E-06
vg1125786354 sf1125320275 11 25786354 3.20E-10 3.34E-06
vg1117255997 sf1116789849 11 17255997 1.38E-09 NA
vg1125885112 sf1125419031 11 25885112 2.44E-09 9.14E-06
vg1126491817 sf1126020231 11 26491817 2.87E-09 2.52E-07
vg1126496401 sf1126024815 11 26496401 1.36E-08 4.12E-07
vg0629541634 sf0629540636 6 29541634 9.75E-07 2.66E-06
vg0916129842 sf0916128841 9 16129842 1.48E-06 7.80E-07
vg0122900714 sf0122899670 1 22900714 6.53E-06 NA
vg0410969707 sf0410960408 4 10969707 7.93E-06 4.33E-06
vg0307012848 sf0307011846 3 7012848 NA 9.94E-07
vg0121726963 sf0121725918 1 21726963 NA 8.87E-06