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 mr1114 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
vg1009043049 sf1008971910 10 9043049 3.50E-19 9.65E-12
vg1008520987 sf1008449849 10 8520987 5.00E-19 2.71E-12
vg1006354247 sf1006369870 10 6354247 8.01E-16 9.17E-08
vg1204314449 sf1204313437 12 4314449 1.35E-15 1.79E-10
vg1005818268 sf1005834806 10 5818268 2.88E-15 1.93E-09
vg0407822984 sf0407818252 4 7822984 3.45E-15 4.05E-07
vg0407824132 sf0407819400 4 7824132 4.68E-15 3.25E-08
vg0905249361 sf0905248361 9 5249361 6.49E-15 8.55E-06
vg1216843191 sf1216837145 12 16843191 1.93E-14 1.20E-08
vg1009170920 sf1009099741 10 9170920 1.23E-13 2.24E-06
vg1009709699 sf1009638520 10 9709699 2.48E-13 1.30E-06
vg0403205910 sf0403201513 4 3205910 4.09E-10 6.90E-08
vg0708524273 sf0708523278 7 8524273 7.64E-09 5.62E-07
vg0501793703 sf0501793686 5 1793703 1.08E-08 3.04E-07
vg1223473790 sf1223440250 12 23473790 2.76E-08 3.47E-06
vg0601673777 sf0601672778 6 1673777 3.12E-08 1.02E-06
vg0308688739 sf0308687677 3 8688739 4.01E-08 4.27E-07
vg0315572376 sf0315571023 3 15572376 1.15E-07 1.55E-06
vg1007452452 sf1007468075 10 7452452 1.85E-07 7.09E-07
vg0619894434 sf0619893437 6 19894434 1.44E-06 1.18E-06
vg0408965989 sf0408961265 4 8965989 1.56E-06 3.88E-07
vg0610429989 sf0610428990 6 10429989 4.50E-06 NA
vg0322604711 sf0322603200 3 22604711 7.80E-06 NA
vg0920481790 sf0920481309 9 20481790 NA 2.45E-07
vg1010541730 sf1010470551 10 10541730 NA 9.76E-07
vg0417689977 sf0417518018 4 17689977 NA 1.15E-06
vg0526662708 sf0526600066 5 26662708 NA 2.80E-06
vg0410583441 sf0410574140 4 10583441 NA 9.91E-06