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 mr1417 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
vg0315312443 sf0315311090 3 15312443 3.11E-11 3.06E-07
vg0330015997 sf0330009036 3 30015997 2.09E-10 1.24E-07
vg1110105406 sf1110099983 11 10105406 7.56E-10 9.51E-07
vg1117964950 sf1117498808 11 17964950 8.30E-10 1.09E-06
vg1110262590 sf1110257167 11 10262590 1.50E-09 8.64E-07
vg0200474832 sf0200474832 2 474832 2.14E-09 3.92E-06
vg1215659438 sf1215656735 12 15659438 2.82E-09 4.44E-07
vg1110108328 sf1110102905 11 10108328 9.37E-09 NA
vg1207087706 sf1207086596 12 7087706 9.42E-07 4.68E-06
vg1119463807 sf1118997495 11 19463807 NA 3.23E-08
vg1215566706 sf1215564003 12 15566706 NA 2.09E-07
vg0626086214 sf0626085217 6 26086214 NA 5.75E-07
vg0200388906 sf0200388906 2 388906 NA 4.72E-06