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 mr1128 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
vg1007617621 sf1007633230 10 7617621 2.88E-14 4.29E-08
vg1006197978 sf1006213627 10 6197978 1.89E-13 5.19E-09
vg0610002564 sf0610001565 6 10002564 8.80E-13 1.49E-07
vg1004296464 sf1004313002 10 4296464 9.74E-13 4.43E-08
vg1008804375 sf1008733237 10 8804375 1.32E-12 1.49E-08
vg0416878791 sf0416706833 4 16878791 3.84E-11 NA
vg0407825281 sf0407820549 4 7825281 6.53E-11 1.56E-06
vg1004879281 sf1004895818 10 4879281 9.36E-09 2.64E-06
vg0207043918 sf0207043918 2 7043918 2.63E-08 4.81E-07
vg0414114398 sf0414105113 4 14114398 1.57E-07 NA
vg1009516560 sf1009445381 10 9516560 3.03E-07 5.91E-08
vg0138427951 sf0138426908 1 38427951 5.92E-07 NA
vg1019398073 sf1019326628 10 19398073 9.99E-07 1.57E-06
vg0135647613 sf0135646570 1 35647613 2.19E-06 NA
vg1019397969 sf1019326524 10 19397969 4.16E-06 6.32E-06
vg0805469573 sf0805468576 8 5469573 NA 2.64E-06
vg0607540736 sf0607539737 6 7540736 NA 2.68E-06
vg0401439086 sf0401434636 4 1439086 NA 4.42E-06