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 mr1609 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
vg1125100181 sf1124634021 11 25100181 2.96E-11 2.96E-11
vg1125604846 sf1125138685 11 25604846 6.07E-09 6.07E-09
vg1124722598 sf1124256438 11 24722598 1.22E-08 1.22E-08
vg1125085942 sf1124619782 11 25085942 1.48E-08 1.48E-08
vg0606540226 sf0606539227 6 6540226 4.53E-07 4.54E-07
vg0218567229 sf0218561360 2 18567229 6.62E-07 6.62E-07
vg0314061468 sf0314060157 3 14061468 7.07E-07 7.08E-07
vg0219377038 sf0219371170 2 19377038 7.47E-07 7.47E-07
vg0430790041 sf0430604914 4 30790041 8.56E-07 8.56E-07
vg0825058570 sf0825055856 8 25058570 1.16E-06 1.16E-06
vg0722742982 sf0722741989 7 22742982 1.23E-06 1.23E-06
vg1014305507 sf1014234273 10 14305507 1.70E-06 1.70E-06
vg1124884095 sf1124417935 11 24884095 2.29E-06 2.29E-06
vg0204941081 sf0204941078 2 4941081 2.30E-06 2.30E-06
vg1101320463 sf1101319464 11 1320463 2.65E-06 2.65E-06
vg1124163322 sf1123697192 11 24163322 2.84E-06 2.84E-06
vg0622673581 sf0622672584 6 22673581 4.16E-06 4.16E-06
vg1125622211 sf1125156050 11 25622211 4.62E-06 4.62E-06