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 mr1212 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
vg0719271738 sf0719270745 7 19271738 6.52E-14 3.00E-09
vg0336255999 sf0336248869 3 36255999 1.12E-10 NA
vg0627263567 sf0627262570 6 27263567 1.83E-10 NA
vg1011075710 sf1011004530 10 11075710 2.04E-10 NA
vg0707895416 sf0707894421 7 7895416 3.25E-10 NA
vg0217211554 sf0217205684 2 17211554 4.38E-09 3.60E-06
vg0409570147 sf0409560845 4 9570147 5.16E-09 9.67E-06
vg0405443357 sf0405438798 4 5443357 3.07E-08 3.50E-06
vg0718872013 sf0718871020 7 18872013 4.56E-08 2.55E-06
vg0431893641 sf0431708536 4 31893641 2.22E-07 NA
vg0216716710 sf0216710840 2 16716710 NA 1.27E-07
vg0103541882 sf0103540882 1 3541882 NA 1.75E-06
vg0812023942 sf0812022947 8 12023942 NA 2.01E-06