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 mr1946 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
vg0406503010 sf0406498453 4 6503010 4.91E-13 NA
vg0912207565 sf0912206564 9 12207565 8.16E-13 NA
vg0500562650 sf0500562650 5 562650 2.24E-12 NA
vg0224529129 sf0224523260 2 24529129 5.58E-12 6.84E-08
vg0118830337 sf0118829292 1 18830337 7.95E-12 NA
vg0501238192 sf0501238176 5 1238192 1.28E-11 NA
vg0232481675 sf0232475806 2 32481675 1.67E-11 1.35E-09
vg1204573883 sf1204572871 12 4573883 3.93E-10 1.68E-06
vg0202558275 sf0202558273 2 2558275 4.35E-10 3.63E-06
vg0722147042 sf0722146049 7 22147042 5.00E-10 5.94E-06
vg0225363637 sf0225357768 2 25363637 9.56E-10 1.42E-06
vg0827046356 sf0827043642 8 27046356 9.98E-10 6.54E-07
vg0403262480 sf0403258083 4 3262480 NA 6.12E-07
vg0220415445 sf0220409577 2 20415445 NA 7.09E-07
vg0220527488 sf0220521620 2 20527488 NA 7.58E-07
vg0432430016 sf0432244907 4 32430016 NA 8.40E-07
vg0420961717 sf0420789772 4 20961717 NA 9.20E-07
vg0415051891 sf0415042606 4 15051891 NA 9.91E-07
vg0138726993 sf0138725950 1 38726993 NA 3.62E-06