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 mr1719 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
vg1201876125 sf1201875122 12 1876125 1.25E-12 1.99E-13
vg0405835784 sf0405831223 4 5835784 6.28E-10 1.68E-08
vg0614114702 sf0614113703 6 14114702 7.62E-10 3.07E-09
vg0918827520 sf0918826520 9 18827520 5.47E-09 5.03E-09
vg0324379515 sf0324377594 3 24379515 1.05E-08 1.28E-09
vg0526295265 sf0526232628 5 26295265 1.90E-08 2.75E-09
vg1017701280 sf1017630053 10 17701280 2.67E-08 2.19E-10
vg0615019600 sf0615018601 6 15019600 2.75E-08 1.27E-07
vg0608352271 sf0608351272 6 8352271 6.60E-08 5.66E-08
vg0719820571 sf0719819578 7 19820571 6.89E-08 2.57E-08
vg0141986897 sf0141985854 1 41986897 1.00E-07 2.61E-08
vg1204320181 sf1204319169 12 4320181 1.42E-07 5.83E-08
vg0526202030 sf0526139394 5 26202030 1.55E-07 1.53E-06
vg0103395359 sf0103394359 1 3395359 4.24E-07 1.69E-08
vg1210620510 sf1210617923 12 10620510 4.92E-07 5.13E-08
vg1219759178 sf1219730648 12 19759178 5.42E-07 2.56E-09
vg0624687317 sf0624686320 6 24687317 2.08E-06 9.45E-08
vg0218459437 sf0218453568 2 18459437 2.93E-06 1.14E-07
vg0412914977 sf0412905685 4 12914977 9.18E-06 2.18E-08
vg0103409480 sf0103408480 1 3409480 NA 2.63E-08
vg0103731353 sf0103730353 1 3731353 NA 3.33E-08
vg1209713133 sf1209710542 12 9713133 NA 1.65E-07
vg1221482713 sf1221449260 12 21482713 NA 4.60E-07