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 mr1889 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
vg0524468976 sf0524406397 5 24468976 2.59E-86 1.44E-21
vg0524593054 sf0524530474 5 24593054 4.12E-86 3.24E-23
vg0915276881 sf0915275880 9 15276881 1.54E-61 NA
vg1021763384 sf1021691860 10 21763384 2.40E-58 NA
vg0110550032 sf0110549008 1 10550032 6.92E-58 NA
vg1224516659 sf1224483113 12 24516659 1.88E-57 NA
vg0524906728 sf0524844143 5 24906728 NA 1.54E-11
vg0623793373 sf0623792376 6 23793373 NA 8.42E-07
vg1122487710 sf1122021581 11 22487710 NA 1.07E-06
vg0124874579 sf0124873535 1 24874579 NA 1.52E-06
vg1100512559 sf1100511562 11 512559 NA 1.52E-06
vg0226120249 sf0226114380 2 26120249 NA 1.54E-06
vg1017012412 sf1016941184 10 17012412 NA 1.88E-06
vg0112525480 sf0112524454 1 12525480 NA 2.23E-06
vg1122554957 sf1122088828 11 22554957 NA 2.73E-06
vg0128489116 sf0128488071 1 28489116 NA 2.86E-06
vg0103576159 sf0103575159 1 3576159 NA 4.16E-06
vg0102964097 sf0102963097 1 2964097 NA 4.79E-06
vg0623793079 sf0623792082 6 23793079 NA 4.89E-06