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 mr1116 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
vg1008520987 sf1008449849 10 8520987 3.00E-15 6.71E-11
vg0407825687 sf0407820955 4 7825687 2.17E-13 3.37E-09
vg1009652418 sf1009581239 10 9652418 2.27E-13 3.29E-10
vg1006294403 sf1006310026 10 6294403 3.05E-13 6.71E-11
vg1005827029 sf1005843567 10 5827029 3.42E-13 1.18E-09
vg1216843191 sf1216837145 12 16843191 1.74E-12 1.60E-08
vg1216843502 sf1216837456 12 16843502 4.67E-12 1.21E-08
vg0528707749 sf0528645104 5 28707749 1.64E-10 1.42E-07
vg0412570492 sf0412561202 4 12570492 3.96E-10 3.54E-06
vg0122848570 sf0122847526 1 22848570 9.16E-10 9.82E-07
vg0223354397 sf0223348528 2 23354397 2.82E-09 4.52E-06
vg0905577010 sf0905576010 9 5577010 2.94E-09 8.77E-07
vg1007140460 sf1007156083 10 7140460 5.08E-09 5.65E-08
vg0610549761 sf0610548762 6 10549761 1.69E-06 2.32E-06
vg0805554327 sf0805553330 8 5554327 1.85E-06 3.96E-06
vg0408293364 sf0408288638 4 8293364 5.71E-06 2.67E-06
vg0610583858 sf0610582859 6 10583858 NA 1.15E-06
vg0300546862 sf0300545860 3 546862 NA 2.96E-06
vg1219268495 sf1219239965 12 19268495 NA 3.21E-06
vg1219269007 sf1219240477 12 19269007 NA 4.61E-06