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 mr1197 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
vg0610027827 sf0610026828 6 10027827 1.05E-08 1.06E-08
vg0610077665 sf0610076666 6 10077665 2.92E-08 2.90E-08
vg0614871126 sf0614870127 6 14871126 6.71E-08 6.73E-08
vg1001247771 sf1001246748 10 1247771 7.35E-08 7.39E-08
vg0207702802 sf0207702801 2 7702802 1.13E-07 1.14E-07
vg1013288420 sf1013217189 10 13288420 1.37E-07 1.38E-07
vg0431675811 sf0431490704 4 31675811 1.40E-07 1.40E-07
vg0915800892 sf0915799891 9 15800892 3.21E-07 3.23E-07
vg0206387400 sf0206387400 2 6387400 4.98E-07 5.02E-07
vg1007756406 sf1007772016 10 7756406 7.30E-07 7.35E-07
vg0611497725 sf0611496726 6 11497725 7.53E-07 7.58E-07
vg0701270264 sf0701269264 7 1270264 7.58E-07 7.62E-07
vg0202747655 sf0202747653 2 2747655 7.65E-07 7.70E-07
vg0517707927 sf0517647568 5 17707927 1.06E-06 1.07E-06
vg0404591448 sf0404587051 4 4591448 1.23E-06 1.24E-06
vg0528854599 sf0528791954 5 28854599 1.24E-06 1.25E-06
vg0212421980 sf0212421976 2 12421980 1.47E-06 1.48E-06
vg0429963778 sf0429778645 4 29963778 1.50E-06 1.51E-06
vg0420179621 sf0420007659 4 20179621 1.90E-06 1.91E-06
vg1207719912 sf1207717316 12 7719912 2.05E-06 2.06E-06
vg0805182138 sf0805181141 8 5182138 2.11E-06 2.12E-06